[V] knew the designations were wrong when they made the game, they've said as much in vartious statements, as well as saying that they had a reason for the system they used. In FS1 they kind of make sense though - I mean, a cruiser in FS1 is of comparable size to a modern cruiser, right? And the only other class of vessel around was something designed to destroy cruisers - a cruiser destroyer, logically shortened to destroyer. I suspect that was close to the logic they used when they made the choices. By the time FS2 rolled around, and they increased the capital ship diversity a little, there was no way to rectify modern classes with the situation they found themselves in, so they picked cool words and used them.
That said, as I understand it the modern definition of words like "cruiser" hasn't remained constant throughout history, and is applied less on scale than on its role within a fleet. Maybe the FS1 cruisers filled the role of a cruiser at some point in the early Sol fleet? And then you're back to the "Cruiser-Destroyer" thing.