Ultimately, the only "fact" we have is that these are the warships that the Imperium chose to build canonically. Why? Who knows?
1) Maybe these ships work with a particular combat doctrine that we aren't privy to. After all, you'll get different results from your High Guard fights depending on the situation you create and tactics you utilize.
2) Maybe there's some political or economic constraint that makes building them this way make sense, such as a shortage of critical components (there's several published adventures built around the idea that certain key military supplies are not as available as the Imperial Navy would like). Or a political treaty limiting certain design options.
3) Maybe a military official or politician influences bad choices by the procurement office.
4) Some other factor.
Or you can decide that the published specs are the published specs and the real specs are classified and include all the fun things you think they should have.
I doubt anyone has played anywhere near enough HG fleet battles to have a good idea of how to "properly" build ships according to those rules. Rules which, btw, explicitly have "ships go boom" as a design goal.
EDIT: Also, if the history of Trillion Credit Squadron is anything to go by, the odds are the "best" way to build fleets is some gimmicky thing no one would expect because these are game rules, not "reality" so are almost certainly possessed of flaws that aren't apparent until played a lot more than they have been.
