Medical Ships are just flying Hospital Complexes, given how large some of the biggest & best Medical facilities are, you probably expect a Medical Ship to be pretty large in general.
Especially a Medical Ship that is designed to cover all aspects of Medicine.
Regardless, it was a dedicated hospital ship (with really large size) and pretty powerful shielding to have been able to hold out against Negh'Var class ships.
You need ALOT of room for everything.
Not necessarily.
As time goes on, technology advances and occupies less space. Same amount of space can be used for multiple other things of same nature.
There is no reason a dedicated hospital ship couldn't also be decently armed on top of everything in say the late 24th century - then again, that class of ships probably wasn't meant to go unacompanied into potential enemy territory, so its possible SF just never installed weapons on it even though it could have.
It wouldn't be the first time SF messed up something that the crew later on had to fix themselves.
The USS Defiant for example had many issues, the primary one being with maintaining high warp velocities because its SIF's couldn't bear the brunt of it - but otherwise, O'Brien managed to 'patch up' other things more or less.
Even with energy transfer from weapons into SIF, it resulted in a 'bump up' at best at maintaining higher speeds.
Sounds to me like the Defiant class should have prompted SF to also design a more powerful/advanced SIF generator (which it may have well done too, we just never got to see that as it could have happened near the end of/after the Dominion war).
Science ships will obviously vary based on their mission profile and what they're expected to do and how deep of a assignment / research they're expected to do.
Everybody's favorite Oberth Class Planetary Survey vessel is optimally designed to map Planetary Bodies and Stellar phenomena.
To my recollection, we have only seen the Oberth performing this duty in ST II, but we have no conclusive evidence that's the only thing it was designed for.
In regards to science ships variations... I agree it will depend on their mission profiles... but its also a bit of a waste of time to expend resources refitting a ship every time its mission changes.
Sure, in the 24th century, this could conceivably be done on the fly without dedicated facilities... in the 23rd though, a bit more difficult (but not impossible to do on the fly).
Although, I am reminded of the fact we had the NX-01 enineers equipping the ship with two phase canons in 2 days vs 2 weeks that were said would take the team back at Earth.
Though to be fair, the NX-01 crew had to bypass a lot of things in order to get things done that way... and even found ways to handle the recoil better than expected.
In short, it worked pretty well, and I'm betting this may have also paved the way towards SF perhaps learning something in the process and integrated in its ship construction moving forward (to at least cut the time needed to finish and launch a ship).
The standard Pontoon sensors was optimally designed for mapping large Spheriod objects by making multiple passes around the planet.
Was it ever mentioned canonically what kind of sensors Oberth used though?
Planetary surveys can probably be done with a single pass around the planet... but the Genesis planet was an oddity given it was created out of Nebula matter.