I think the Season 2 one was just an FX error, and none of the other ship designs have torpedo tubes on their nacelles.
There's no preferred launch point for torpedoes in any of the fight scenes for any of the ship designs, because there are no sufficiently prominent exterior features in any of the ships for the VFX artists to associate with torp launch (compare, say, with the prominently red-lit phaser turrets that are unerringly used). The hero ship fires torpedoes in "Into the Forest" from basically everywhere - when we get the head-on view from behind Kol's controversially bald head, some torps come from below the
Discovery saucer, some from above; some from the centerline, some not so much. It is no consolation, really, that none come from the nacelles or their pylons there.
Perhaps we're best off thinking in TOS visual terms: torpedoes are not "fired from tubes" as much as they emerge quietly from the ship by unknown means and
then light up some distance from the hull, possibly at fairly arbitrary locations following the actual deployment from a non-arbitrary deployment doodad.
Might be this is how you fire a volley: you deploy masses of torps from a couple of chutes and have them spread out, and then they all separately ignite some distance from each other and the ship, so as not to mutually disrupt each other or the ship. As technology progresses, you can light 'em up with less and less delay, until ultimately they glow right after emerging from the tubes, making the tubes themselves stand out as the points of emergence.
In any case, if these things are charged with antimatter, having the launchers close to other antimatter-reliant machinery might actually be a good idea: you can concentrate your protective measures, or banish the kaboomables to a small number of peripheral locations. I don't think there are tubes in the nacelles of NCC-1031, but there might indeed be tubes in the pylons right next to the nacelles.
Will PIC do any differently? Depends on whether the hero and villain ships are designed with prominent weapons emplacements. If the torpedo tubes are nondescript dots on the hull, they probably will go unused or misused. If they are giant barrels the camera is keen on zooming at in the pilot episode already, later misuse is unlikely.
Timo Saloniemi
SC. They literally mount the forward Torpedo Launchers in the Warp Nacelle, it surrounds the Bussard Collectors. They literally have video evidence of it in ST;DSC.
