I didn't realize that some (most? all?) soil has golden skulltulas hidden if you drop bugs in there. I've already planted magic beans in a bunch of places. If I've planted a magic bean in a place where a golden skulltula can be found, would I still be able to get that skulltula or is it lost forever?
Yes, you should still be able to get the Skulltulas after planting the magic beans.
Even though planting Magic Beans in soil will help gain access to different areas, there is another use for the soil. Link can bottle some Bugs and drop them into the soil. This will result in a Gold Skulltula jumping out. This can be done even after a bean is planted.