I don't play combat so all I can base these ideas on is what I've read.
The way I see it, unlike real life, games have obvious defined limits. If possible players will put their heads together to come up with counters to specific strategies. Sometimes a strategy is so lopsided it undermines the entire point of the game. At those times I believe it's when the devs should step in.
This brings to mind some sort of logic controlled automatic scanner network. This, combined with turrets, could be used to shine the light on pesky cloaked warheads. To overcome this neutral warhead deal, perhaps it could be coded so they need to be manually armed and the only way to do so is by having the warhead set to a faction. If the player gives up the faction on the warhead it immediately disarms. An alternative is for the warhead to immediately give off a hostile signature when armed. This would bypass the need to always faction a torpedo while still allowing them to be targeted as a hostile entity.Now, using a cloaker tipped with buffed warheads to ram your ship, could be considered griefing, since if you're outside your claimed system, you get absolutely no warning of a cloaked ship around unless you frequently tap your scanner (if you have one) and hope you randomly catch someone who might as well arrive and pull the stunt off between 2 scanner recharges. Again, it's a MAYBE.
The way I see it, unlike real life, games have obvious defined limits. If possible players will put their heads together to come up with counters to specific strategies. Sometimes a strategy is so lopsided it undermines the entire point of the game. At those times I believe it's when the devs should step in.