I think the hashes of the two NANDs are different because the NAND is used between the two backups and so there is a slight change.
It's different to a backup with a hardmod because you don't use the 3DS between those two backups.
I think the 300 title limit is not simply a number in the home menu. It is based on the fact, that the ticket.db has a fixed size, that has only enough space for 300 titles.
If you have arm9loaderhax with updated sysNAND you should first boot into 9.2 emuNAND by pressing L on boot. Then launch Gateway without the GW-Card, then insert GW-Card and press B while you boot sysNAND in GW mode.