One would assume that all the players in the 24th century would be well versed in the general capabilities of a starship or an armada of starships, and would prepare defenses accordingly. Precision strikes could be negated by hiding the industries or (in the case of certain threats such as the UFP Starfleet) by extensively using civilians as shields. Industries would probably also be rather distributed; one could even imagine a war industry operating on the household replicators and transporters of a city, while the civilians would still live in those households and just get their food from central kitchens.
Then we have the Breen strike against Starfleet Headquarters. Apparently, it achieved next to nothing: instead of biblical-level destruction, we see tiny craters, thin pillars of smoke and some charred buildings, plus of course symbolic damage to the Golden Gate bridge. Does this mean the Breen only wanted symbolic destruction and carefully avoided using any of their usual weapons, merely firing dedicated harmless firecrackers to send the message of "these could
have been antimatter warheads and this could
be a crater deep enough to spew magma for millennia, but we aren't the sort of bad guys our partners-in-war are, and please do remember that at the peace negotiations"? Or does it instead mean that San Francisco and other cities have defenses that turn the awesome destructive power of a standard starship death ray into this harmless show-and-tell?
Destroying of entire planets was a novelty for the Dominion; apparently, they appreciate captured planets enough to avoid destruction in the usual case. Attacking Starfleet HQ was unheard of as well - but there we didn't learn why this should be. Granted, the Breen attackers didn't survive their heroic mission, but surely Klingons and Romulans would be ready to perform suicide strikes as well?
In a Federation/Romulan conflict, symbolic strikes of this sort might well feature heavily, considering how Romulans always want maximum effect from minimum effort and go for fancy precision plots instead of frontal attacks...