It's annoying, but there are workarounds (none of them really pretty though):
- Cut a hole in the removable battery cover/bottom lid where the uSD slot is so you can get to it whether it's on or off
- Dremel out the screws on the battery cover so they're not there anymore, making it easier to take it off (I know you can leave it on unscrewed, but sometimes they get kind of stuck)
- Get one of those weird uSD extension cables from AliExpress or whatever site had them, and have an easier to access uSD slot that sticks out of your console
I suppose one could also try removing the game card slot and relocating the uSD slot to there. No clue if your N3DS would still boot after that though.
That, or relocate the uSD slot near the charging jack or somewhere else.