The E-E has one in Nemesis as well. In any event, at least after the events of "Heart of Glory" one would think that a 'lesson learned' would be that more security measures are needed with regard to the warp core.
...yeah, yeah, it's a TV show, and the E-D has multiple security failures throughout the series, and if their security was all it should have been then several of those episodes wouldn't have even been possible to begin with...
I was only thinking of the tv shows because budgets were a bit more restrained than a movie, but yes, NEMESIS had one around the warp core, too.
I was thinking of instances where the computer on the Enterprise-D was taken over/hijacked, and while rare, it did occur.
"Home Soil" - 'microbrain' took over part of the computer system while it was in the lab.
"Evolution" - the nanites, after Dr. Stubbs killed a bunch of them, purposefully made the air toxic on the bridge.