GMST stands for "game settings". In straight Morrowind (i.e. without Tribunal or Bloodmoon) these aren't of any consequence.
With the expansions installed, however, they
can cause problems, probably because Tribunal and/or Bloodmoon change these settings. I don't know.
Thus, when releasing a plugin, one has to use a third-party program like Morrowind Enchanted Editor or TESTool to delete these entries. Otherwise, names of things can go strange, quests can break, moving objects can double, among other problems.
Here's a page that explains a bit better.