<<A battle between the seaQuest and an automated submarine in Season 2 played out like your usual TNG battle. Some fancy maneuvering, a beautiful but slow shot of a vessel cruising, firing one sustained energy attack, and much of the additional action happening via dialogue rather than on-screen special FX.>>
Firing energy weapons? Underwater?
Yep, definitely. There's a good clean scene of the seaQuest firing energy beams not unlike a green version of the TOS Enterprise phasers. The episode is called "The Sincerest Form of Flattery" in Season 2, about the seaQuest battling an automated submarine programmed with...
Bridger's mind! (don't you just love those campy second season episodes?)
The vessel's energy weapons become more prominent later in the season and in S3, when the show becomes more action-centric.