In the first wink out, people noted the loss and that's why you have Masters checking in with Kirk.
Yes, that's my point: that's how you notice problems with dilithium that is being used by the ship.
Does your point also include that the time from the crystals were drained in the first wink out and the time Masters shows up on the bridge is at minimum 4 minutes? (2 minutes + intro + 2 minutes on planet surface). Put it another way, in each instance the crystals were stolen afterwards the crew already knew something was up with the dilithium and therefore they didn't need to report it immediately or the time for them to report it was well after the action and scene to be included where the TV viewer could catch it.
The other times the ship was alerted to a situation to the dilithium as it was happening so if it was a problem they would've noticed. If not then they could of been idling those crystals.
And that's how it would go if the dilithium indeed were "idled". But it's not: it's being reamplified, and has been fully reamplified when the thefts take place. It's off the loop in some other manner, or then reamplifiying means zip and, more generally, dilithium means zip.
On the contrary. According to the episode they were already re-amped before we see them stolen from the energizers yet we know the ship wasn't actively using full power.
It's the same in "Elaan of Troyius". The ship went to red alert with an attacking Klingon battlecruiser but nothing on the ship yet was pulling power to the warp engines or phasers and therefore no one knew the dilithium crystals were going to be a problem.
Those crystals in the energizers were reamped and were immediately available for use in the energizer even though the ship wasn't actively using them yet.
But the first wink-out established that reamplified dilithium is crucial instead!
It only established that they needed full power
in ten hours before their orbit will decay. For all we know once they were reamped, they nudged the orbit and reset the clock.
KIRK: You have a talent for understatement, Lieutenant. Without full crystal power, our orbit will begin to decay in ten hours. Re-amplify immediately.
The crystals had already been reamplified before Lazarus steals the first pair so that would mean the energizer we see them in is already being used for powering the ship.
Well, that's a good alternate take on it. But it doesn't get around the problem of why something crucial to the ship's survival, that is, whether the crystals are in place and amplified or out of place or drained, would no longer be constantly monitored.
It probably is constantly monitored. I just think that the TV viewer isn't always informed of the situation immediately because the action is occurring somewhere else away from this specific chain of information.
After the 1st wink out - 2 minutes go by on the bridge before Kirk and co beam down and only when he returns to the bridge does Masters give him a report. We can speculate that all sorts of alarms went off with the crystals drained and the engineering crew informed Kirk on his way to the transporter room and Kirk had Masters report to him when he got back.
After the 1st crystal robbery, Kirk already knows that Masters is being attacked and his immediate log entry states they lost 2 crystals. Again, the tv viewer isn't shown the intervening time where they go over the power loss, inspect the energizer, etc.
And again the 2nd crystal robbery with the shorted energizer, Kirk and co enter and confirm the stolen crystals. Again the tv viewer isn't in on the chain of conversation about the lost power because the show cuts to Lazarus in the transporter room.
Both cases that you are arguing about are covered:
Q. Why aren't the crystal power loss noted?
A. They were in the first case after a long delay. In the remaining cases they didn't have to show the tv viewer because the loss was already noted.
Q. Why aren't the crystal power loss felt?
A. The ship's crystal converter assembly and systems were undamaged and the ship was not doing anything high powered in each case. We've seen the ship go to Red Alert with shields and still not trigger the use of the crystals ("Elaan of Troyius").
Well we know only the warp engines regenerate and the impulse systems do not so that's main power being regenerated forever

Also remember Kirk gave a more finite duration when it came to food supplies versus the forever of their power situation.
To nitpick, Kirk was
about to give an estimate for the food supplies, at which point Odona substituted "forever". We don't know if he was about to say that food would outlast energy or vice versa - but from the lack of comment, we can rest assured both would outlast the two castaboards, to it's academic only!
Nitpicking your nitpick, here is the dialogue where Odona asked first about "forever", not afterwards:
KIRK: How long would you like it to last?
ODONA: Forever.
KIRK: Well, let's see. Power, that's no problem, it regenerates. And food. We have enough to feed a crew of four hundred and thirty for five years. So that should last us.
And Kirk is very specific here about the "forever". Power, no problem it regenerates. Food, not forever, but enough for the two of us.
What piece of dialogue has "warp energies regenerate"?
In the TOS dialogue, only warp engines are ever mentioned to be able to regenerate or need to be regenerated.
As for "antimatter generators" or "matter/antimatter generators", an analogy to "diesel generators" would have these consume rather than produce antimatter... And would be consistent with the idea of antimatter as a versatile onboard power source, used both in the main reactor and various other applications down to photon torpedo warheads.
That's one way to interpret it. Although the in TOS having a m/am generator on the ship making more m/am is inline with how the series is presented.
Now, the background assumption in VOY was that they could increase their onboard antimatter supply with a doodad they had aboard - a doodad that required fuel in order to run, but then basically converted that fuel into the sort that the warp engines could use, that is, antimatter. All of the adventures make sense with that in mind, even "Deadlock" where the total loss of antimatter from one ship would be something it would take ages to replenish, and not an issue they could solve with the doodad in plot time. But direct dialogue support is more or less lacking.
That dilithium would be fuel is an idea not well supported by any of the adventures, even if dilithium is crucial for getting oomph out of fuel. But the Hansens could be cutting corners in the dialogue there, saying that ramscoops can get deuterium from any old gas giant, but only those systems with additional resources such as dilithium are relevant as potential fueling spots...
Or perhaps the Voyager writer watched a TOS episode and thought, yeah, get some more dilithium and use it to create some m/am fuel.
