Yes, the H90 can certainly process two instruments at once. This is best done in the Dual routing mode where Path 1 flows from I/O 1 and Path 2 flows from I/O 3. For a deep explanation and setup I recommend this video:
No, because I/O 3 is used for connecting an insert effect in the default mode, which is Insert mode. In this configuration, only In 1 acts as the main input of the signal chain.