The interesting issue about "Mudd's Women" is whether just one or several crystals are in active use at a given time. We don't see the heroes suffer from a visible "hiccup" of power when each of the crystals blows, but OTOH we don't see them suffer from a stepwise loss of power, either. So it could be that just one crystal at a time is "running", and when it blows, another comes on line very quickly (it's on a "circuit" of its own, waiting, and a simple flick of a switch selects a fresh circuit as needed), and the power is kept steady; using multiple crystals doesn't give more power, and may not even be possible in the first place. When a single crystal fails to give "full" power, this may be attributed to the cracks in it, rather than to the lack of multiple parallel crystals.
Compare to "Alternative Factor", then. The universal hiccup drains "almost all" of the crystals. We don't learn whether these would have been hooked up to machinery or waiting in storage, or perhaps being "active spares" already dumbwaitered into the machinery but still waiting for their turn to serve at the m/am reaction focus. Kirk needs "full" crystal power, but does not explicate whether this calls for multiple crystals, or merely for a single non-drained one; naturally, he would order all crystals "re-amplified" immediately in both scenarios.
Yet when the first Lazarus steals two crystals, Kirk exclaims that with them missing, the ship cannot operate at full power. Of course, even with the theft of two more and the apparent loss of the energizer room, the ship still retains the ability to orbit, to beam people up and down, and to fire weapons... But it does appear as if a fairly large number of (paddle-type) crystals are needed simultaneously to yield "full power". Not so many that two would represent an insignificant fraction - but not so few that loss of two or even four would completely deprive the ship of power.
Since just three were lost in "Mudd's Women", and the ship still struggled, we're probably speaking of a fairly fuzzy system here. Just one will give warp in a cinch; something like six may be on line simultaneously
for maximum power and flexibility; and Kirk can live with having four available, for single or simultaneous running, but will be quite worried when facing a crisis with a minimum of (still partially drained?) two.
Perhaps the parallel use of crystals for "full power" doesn't mean they are all active? Perhaps it just means that Scotty will not have the courage to throw the lever on the single active crystal to "full" unless he has at least three fully amplified backup crystals available in the reactor system?