Okay, in more recent books, we find out that the DCMS for example, had destroyers and that one Samarkand class in orbit--but they were declared as being impossible to reactivagte during the clan war. But they had been mothballed (not very well) due to expense.
But you don't do that if you think you're going to need a weapon-- you keep it, whatever the cost.
Secondly, the lack of transit drives doesn't make much sense--even in 3025 the Successor states were beyond age of war technology and the first warship drives predated that era. It would have been difficult, but it wasn't anything like trying to upkeep star league technology.
So why did they vanish? I'm going to go with a more or less unofficial agreement.
1. The fleets of the successor lords *did not secure victory*. In the end, the ships were lost, by and large maintaining a stalemate or limited victory.
2. More so than any other conflict, their fleets proved vulnerable to being destroyed.
As a combination of one and two, by the end of the second succession war, Warships could very well be seen as being a more or less bad investment--but one that you might need to make if the other side had made it.
However, because of the destruction of the various warship yards, no power was in a position to build new warships and any attempt to do so would be noted, allowing the other states to either attack it before it was ready, or build their own warships.
However, to do so would be eocnoimcally ruinous, so the various states more or less came to a "I won't build it if you don't" agreement. As the third succession war continued, and the doctrines of limited conflict and war by maneuver rather than war to destruction, new generations of officers grew up, and what had been a pragmatic arrangement became more set, simply because most leaders and admirals saw the kind of war exemplified by the warship fleets to be both wasteful and ultimately--futile.
Attempting to explain it in universe, with economics, will just kill catgirls. We can extinguish them up through 3025 by assuming loss of means of production - all the population in the 'sphere wont build you a compact core if noone knows how to build compact cores.
But by 3050 that Memory-Core Powered Cat Girl was out of the bag, and nothing can put it back in. Houses WERE cranking out warships, though with fumbling baby steps as they work out the kinks and bring yards back online.
Then the PTB used the Wobblies to clean up all the warships and their factories (barring of course the Clans, cause... Clans). This gets your numbers back under control for a while.
But between the Jyhad and 3145? I got nothin. The knowledge base exists. Warships are proven to be terrifyingly powerful, and Snow Raven and Ghost Bear are known to HAVE the things. My only guess is the Succession Lords assumed that, no really, this time we mean it, the wars are over and the good times are here and it will never happen again.
The justification for a lack of warships is that the game is called Battletech and its about Mechs, and the PTB believe that Warships will take away from mechs (A proposition about which I have opinions, but no proof - and if I wanted to make those decisions, Id make a lot of money and buy the company. And probably run it into the ground). Heck, the MECH numbers can only be explained in the 3025 era.. everything after that exists in a tension between 'Lets upgrade and pretend weve got real militaries run by people who care about winning' and 'War as Sport of Kings and YOUR DUDES CAPTURE WORLDS'.
This was chosen in favor of Your Dudes. And once youve decided that Your Game is about Your Dudes, sacrificing that aura (and sales) in the name of having the universe make sense is a fools errand. For ever BTech player that scratches their head and goes 'hunh', theres 100 more who just want to play the game, and they buy books too. They are, and as a buisness case SHOULD, be the focus.
So if you want warships, economics, science, or logic, write an AU. If you want to make money selling a game about stompy robits and YOUR DUDES, write Battletech.
This is not a criticism. If they want to keep the company going (and we want them to), you have to make money.