This issue is separate from both Luma3DS and TWilightmenu. What do you mean by "hangs" exactly? As in taking too long to boot into the home menu, or in booting into a black screen and staying there?As I said i also sometimes get hangs when booting the 3ds when my sd is plugged in ( the one containing the mods )
Do you have a large sd card (+64GB)? It could be because of the cluster size if it's set to 32kb (if it's a large sd card). The boot will be slow, like up to 1min..