Weapons Quality

do deactivated weapons still lose there quality or has that changed? and also as a side note do Navy missile batts and Navy interceptor batts protect targets in your country like cities if they are close enough or just the navy itself?

Deactivated weapons do lose Q over time. And navy batts do not protect country targets, only the fleet/carrier they are assigned to.

ok... is the quality loss significant? or can it easily be brought back up with upgrades?

It becomes significant over time, but yeah eventually it can be raised.