Whew, that was a long subject field...
There are a couple of ways to deal with this, which can be used jointly:
(1) Consider the 1 hardpoint per 100 tons a *legal* restriction, not a design
one. Military and pirate ships ('What laws?') do not have to obey this
restriction. However, to keep some sanity, perhaps limit the volume of weaponry
to 10% of the ship's volume. This includes turrets, spinal mounts, bays,
whatever.
(2) Merchant ships must use weapons of a lower technology than what is
available for the military. It should be at least 2 TLs lower, perhaps as much
as 4. Pirates will fall in-between the merchant and military ships, since they
will loot weapons off of whatever they can. This should also apply to armor,
and other offensive/defensive items.