One thing you'll want to keep in mind is that fleet defense modules stack. In a scenario where you have the resources to carefully design ships specifically for a fleet, you're better off equipping everyone with barrier field generators and field augmentation arrays versus having everyone pack their own shields. Point defense fleet modules aren't as good, but depending on your tech and what you're preparing for, they may still be more efficient than pure individual modules. One sneaky issue is that a ship cannot benefit from a percentage based booster such as the field augmentation array if it doesn't start with its own shields. Therefore you'll want each ship to bring some of their own shields and point defense. If you're using carriers, the ability to project shields and point defense onto your fights can be useful as well. However, there's no way to project raw armor points onto ships with fleet modules. Unless you're willing to use military starbases to provide armor for your fleets, each ship will need to pack their own armor. The subsequent math for then determining whether the percentage based armor fleet boosters are worth it isn't straightforward, because that mass could be used for other unrelated things.
If you're in an endgame scenario where tech trees are filled out, I don't think it's worth investing much in defense. There are too many ways to ignore defenses. On top of that, it's far easier to ramp up damage, so it's better to also focus on range and weapon cooldowns, so that you're shooting first and faster. Unfortunately for this purpose, fleet weapon modules appear to be nonfunctional at the moment.
As a miscellaneous tip on the subject, once you get fleet based movement boosters, save mass on your ships by swapping out engines for stellar accelerators. This costs promethion, but if you're taking the time to build a very strong fleet, you may as well go all in and give it a long reach.