Heh, yeah, 3 things.
First, every room in the vaults stays dead once you beat it. I'm not that cruel.
Second, check out what I said to ms_lady_zelda a few posts up, about getting the whisp ring. If you buy it for 225 in the ring shop at the far south-east of the desert area (the one you come past after going out the back side of Spider), that will remove permanent bubble disablements in like 2 seconds, so those yellow bubbles will be as harmless as the regular static bubbles.
Third, Desert also has Farore's Wind, so you can warp back to the start if you fall down (if F6 feels like a cheat, though it really accomplishes the same thing anyway).
Also, these side-dungeons aren't really required for the following areas anyway, so if you want to go west and hookshot across that lake to the next area first, pick up some more hearts and magic and maybe the magical sword and possibly even the 1/2 magic upgrade before going back in there, that's a good idea too.
(And FYI, pits in normal dungeons are never traps. Only side-dungeons.)