I would like that limit gone too. It's actually worse: for ships that can link three banks, the maximum delay is 2.5 seconds. For fighter-mounted beams, warm-up/down and lifetime all cut into that, too.
Using energy or ammo as limiters has its own problems. Both(?) depend on the number of gun banks, energy regeneration is by default scaled according to difficulty, and ballistic weapons can (or must be, depending on which you consider the drawback) be reloaded.
I think the best place to put it might be in AI profiles. Then modders could easily enable it on a per-mod basis, or disable it for debugging (which, as far as I can tell, is the only reason for the limit).