Yes because it's not needed and won't work when Tiramisu is loaded (I think, but you won't need it anymore). ONLY do this for the NORMAL Haxchi, NOT Coldboot Haxchi. CBHC must be uninstalled through the CBHC-Intsaller first.
CBHC must be uninstalled, but normal haxchi may be useful.
If I'm not wrong, if you eject the sdcard or it's no longer readable, tiramisu will perform a non-cfw boot. Haxchi doesn't need any sdcard therefore you could launch it to get cfw.
@Maschell is there any plan to use the internal storage without any sdcard? In the 3ds scene, the luma cfw allows booting from sdcard and from nand, the former with higher priority.