The N100 only has 9 gen 3 PCI lanes. The board has 4 USB ports (2 x 3.0), 4 2.5G ethernet ports, 2 m.2 slots and 6 SATA connections. They might be using a PCI splitter chip to connect all components, which depending on the type and how it’s used could have a big effect on I/O performance.
EDIT: The N5015 from your previous board only has 8 lanes. What was your max read/write speed on it and did you see anything strange in lspci?