I don't know if this has already been addressed as I haven't really looked at the SCP at all (just been playing non-SCP campaigns). But one thing I found really dumb and annoying about Freespace 1 + 2 is that when you fire a secondary like a bomb from one bank, and that shot depletes that bank to zero, then the delay is transferred to the next bank.
For instance, if you have Helios in sbank1 and Hornets in sbank2, and you fire the 2 remaining Helios then the Hornets have a 20 second delay before they're fired or something.
This has always struck me as super-dumb. Firing delay should simply not transfer over to unrelated missile banks on the same craft.