To be sure, none of the USN combat-capable vessels today sport combat-capable boats; such auxiliary craft are only found aboard the combat-incapable vessels such as amphibious assault ships, to complement their capabilities. There isn't a known mode of naval fighting today where an armed boat would be of help for an armed ship or vice versa.
Also, exposed nacelles have never been shown to be a combat liability in Trek; only failure to protect them with shields has. And exposed nacelles may well be a combat forte, as the one thing where the Defiant was quite inferior to generic Starfleet ships was speed. With better, exposed engines, she might have outrun pursuit in key episodes such as "Way of the Warrior", or gained on adversaries or reached battlefields faster in others such as "For the Uniform" or "The Die is Cast".
Timo Saloniemi