Hmm, that's a weird one, I cued it up, it's there, but you can clearly see there's no possible location for such a thing. Also, in the script, the Klingons are talking about emergency power when they mention the line, so it could be a reference to power rather than the tube (which, BTW, in the long shots doesn't have the lid, but the tube is more outie than the Corgi version - my guess is they made the lid on only 1 size of fx model rather than all of 'em). As for the tube, I'd chalk that up to a script mistake or the modelmaker didn't understand what needed to be there for that line to be accurate.
I bet there is a reserve photon tube somewhere it just hasn't been located. Each BOP like from ST3 "D11 class" has an emergency tube. Check this article out.