[I'm assuming that this is an N8x0-related question, because modprobe works on the N900]

A depmod binary that works on the N8x0 can be found here.

I don't have my N8X0s around anymore to verify, but I believe the modules from /mnt/initfs/lib/modules needed to be symlinked to /lib/modules/current so that depmod would see them. Something like that, anyway.