Nickel has always needed an USBMS session to index/update books.
I can't vouch for it looking inside /mnt/sd on devices without an SD card (EDIT: Actually, it probably does, c.f.,
#10), but, for the rest, may I interest you in our lord and savior NickelMenu's
rescan_books feature, which will allow you do to just that without actually going through the hassle of an USBMS session

. (Which you can also fake via NM, BTW ^^).