I agree - the thing I'm working on is going to greatly reduce the amount of damage you can do to a planet with bog-standard ship weapons too.
A good compromise would be to add smaller base sizes that can be used as cheap orbital weapon platforms (give them a big maintenance reduction too), but you can't stick them in a freighter and reinforce a new colony (not necessarily a 'bad thing') as you can with planetary-based platforms.
Also, if you remove weapon platforms you might get more troop v troop (plus militia) ground combats, which I'm all for.
Here's a link to
Fyron's modding 101, which I found very useful.
The cargo storage figures are best treated as being arbitrary. There's nothing stopping you from changing them radically. I think in Proportions your homeworld can store a huge amount of kit.