Revert "Tools: skip check_submodules.sh when NUTTX_SRC is set"

This reverts commit ac8f179f2dad99d664a6f9de4df954bea7fe5858.
Tools: skip check_submodules.sh when GIT_SUBMODULES_ARE_EVIL is set

this avoids using submodules when a specific NuttX tree is specified
Updated submodule update instructions