Practical concerns militate against having a homogenous force of 12 of each every time.
We know, for example, that the GTVA isn't shy about issuing non-homogenous gear within a squadron or even a wing (they let you do it all the time) and it's unlikely those fighters are being taken from another squadron's roster of active fighters and made available to you. (It's even more unlikely you're being allowed to borrow them pilots and all.) I can think of a half-dozen ways that would cause people to have fits. This implies the GTVA carries significant pools of spare fightercraft aboard a destroyer, and considering how badly you can have some of your squadrons get shot up in a mission and yet be at full strength the next, significant pools of spare pilots.
Squadron size is to some extent more dictated by the number of personnel required to make up a squadron than the number of ships. Different fightercraft require different amounts of maintenance. Bigger ones require more people to see to their needs than smaller ones; more complex ones require more people than less complex ones. This is an important concern because it's necessary to have squadrons be interchangeable. This allows you to tailor the squadrons being sent with a ship to the mission, and to replace squadrons that have been shot up with fresh squadrons even if they're not necessarily the same type, getting more fightercraft to the battle zone. If you can't house enough mechanics for a medium bomber squadron in the space your interceptor mechanics took up (or the other way around), this is a problem.
Lastly, some types are simply more useful than others. You need more fighters than you do bombers, because fighters are required for strike escort, fleet escort, and destroyer escort, as well as offensive fighter action like sweeps or raids against enemy escorts. Certain types of fighters are more flexible than others, to boot. Medium bombers can be profitably employed against anything from freighters to destroyers, but it's not worth getting a heavy off the deck for anything smaller than a destroyer. You must be able, during wartime, to shuffle squadron size about in response to these things without having to redesign your hanger or crew decks.