I know there's a guide on wiki, but I didn't quite follow everything

what's the point of uping the level of the beam weapons (the damage doesn't increase, but the price goes up)?

and I like the fact you can change the torpodoes and tubes, but can you change the beam weapons? (for example, change that phase emitter into a disrupter?)

uping beam level increase the range of the beam - that's the advantage. (There's no change in damaging or rechargetime)

I don't know/don't think there's a option to change beam type ingame - but as e.g. Coalition "Belvedere" replaces "Peraine" ship the higher ship class Belvedere has better beam typs

MODDING:
Of course you can mod shiplist.data by shipeditor, change there the beam typ and than you have to start a new game (shiplist.data always is a part of the sav-file, no changes make effect while a game is running) -> but I think you wanted to change beam type ingame