This was just my experience, but I found hydra and detritus inside of rock wool in pots. I'm not saying they come with them or cause them, but they are a place for those buggers to hide.
Stripping rock wool can be difficult to do safely depending on the plants root system, but I recommend it.
Planting in substrate came be difficult with some plants. With species that like to be rooted in substrate, but don't take easily, you can fashion a paperclip into a v shape, then bend the legs in half like knees and it'll act like an anchor for your rooting plants. Otherwise fishing line ftw when attaching stuff like java fern that doesn't do as well (or will die) if planted in substrate.
It makes the tank look a lot nicer too, a bit more work, but well worth it imo