My first reaction when being notified of the bug from the fix is to just change the code to allow #weak weapons to not be culled out by the fix and that prevents issues with both the retail FS1 and FS2 missions. But as Goober pointed out, when he and I were talking about how to address this, some people are making use of Shivan weapons which also aren't "player allowed". I hate having it broken like it has always been, but this is the type of thing that I quickly bow to from people who no more about how this stuff is actually used by mod/mission makers.
But, if you or anyone else wants to voice your opinion on it then go right ahead, Goober may agree to just go with the #weak route to fix the FS1 and FS2 missions, and then everyone else will just have to fix their tbls/missions if they have other such instances of doing-the-wrong-thing. My opinion should be obivous (as evident by the code comment for removed fix "disable this bug fix for now, too many idiots taking advantage of it"), but I'm going to go with whatever Goober wants to do here.
There isn't a Mantis bug on this exact issue, just the one that ended up causing (you responded to that bug btw, #1196). That bug was about a weapon that, when you clicked on it in the weapon loadout screen, would crash. The problem was that the weapon wasn't "player allowed" and didn't have all of the required tbl information to work in the loadout interface. But, since FRED doesn't show such weapons, it wasn't obvious what the problem was since you couldn't do anything about it. Only after noticing what the weapon actually was and figuring out that FRED wasn't showing everything in the weapon pool, did I realize what the problem was. Hence the fix that was made, to force everything in the "$Weaponry Pool:" list to actually require the "player allowed" flag. FRED was also changed to detect this problem, notify you of it, and then automatically fix it so that when the mission was re-saved the problem weapons were removed from the pool. Currently, the only thing that actually cares about "player allowed" is FRED itself, then normal game doesn't really care about it.