Two points:
They were recreating the original and that was basically CVN in space. Yes, it had some secondaries that could be batteried to do some damage, but it was fighters that kept the enemy fighters off the ships of the fleet, including the Galactica, in both shows. And fighter guns could take out or cripple civilian ships and enough of them could even cause critical failures on a Battlestar (in the original).
When they redesigned the new look, it had to still have that character, but with a solid look and feel borrowed from CVNs and Battleships internally. That's likely what drove the aesthetic. The fact the Galactica (2003) could take a right whaling and still keep rolling ahead was somewhat in line with prior canon. The fact it had nuclear missiles of their own was sensible (given the Cylons had them).
I do agree fighters were important screening and area defense assets. However, if one side lost the fighter battle, then they could become (with losses albeit) ship killers with even modest luck. I think they would not have been as good at killing military ships as a Cylon Basestar in the new iteration so those were willing to join in and shoot it out to try to take Galactica out (and thus end the Colonials forever as the rest of the fleet could be taken piecemeal).
The cylons used missiles more often and I often suspect that was a stylistic/plot choice rather than any form of doctrine (the doctrine, if it was stated, grew from the dramatic benefit of missiles - guns blow you up fairly immediately, missiles you can run, flee, dodge, jink, distract, etc. and that sequence makes for great action and lets your heroes live more often).
I also suspect we can't know how much tonnage was devoted to armour - I suspect a lot - they had a lot of internal shock frames and bulkheads and that is one manifestation of armour (as Traveller does not make itself concerned about internal structure at least in the earlier generations... not sure about T5). We do agree that their fuel requirements for jump were lower (though non-zero) than those in Traveller where you not only give up a lot of space to jump fuel, but also to jump engines on large ships.
There is a big risk that larger ships have (noting they do have, in some configs, real volumetric advantages): If something bad is to occur that means the ship is going to expire with a bang, the majority of crew not at the surface would likely never get to escape successfully. Ships with a less deep core might see more survivors. That's one of the few downsides I can see other than limitations on weapons mounts for big round death balls where a cylinder format or rectangular prism layout would give you more surface area for weapons mounts.
In the real world where people pay for things and politicians make that happen or don't, many procurement decisions are made for non-technical reasons and the doctrinal reasons sometimes stem directly from the realities of budget as much as sound military thinking.
My brother-in-law and his wife are both high functionaries in RCAF procurement (educational!) and another friend of mine was USCG with enough visibility to shake his head at how the USCG went about deep water vessel procurement. And my godson's dad explained to me one time why the coastal defense boats we bought lasted half the expected lifespan and why new engines were costing us a mint - cheapest bidder then upfits to be operational which overloaded parts of superstructure which caused superstructure failures under the pounding conditions in coastal waters... all stuff that was the result of crappy procurement largely driven by budget, not efficacy or even fleet doctrine. We bought Aussie used F-18s to extend our fleet's life until we complete the second (or maybe it is the third) 5th gen fighter re-specification, contracting, and acquisition (if it ever happens and we don't go directly to 6th gen). That was totally dictated by politics because politics repeatedly gutted the purchase of the F-35 even though we could have had those and be operational with at least some of our order by now.
I don't see the Travellerverse being any more free of budgetary and political impacts in large military procurements. Given the nobility in the picture, and large military-industrial mega-corps, I can totally see all sorts of lobbying and chicannery as well.