Hi,
some things are not clear to me:
* Where is the PC at your drawing?
* is the PC used as USB_host for data transfer?
* "The second set of electronics".. is it Master, slave, OTG? Or just something that needs power without data communication?
1) if data lines are connected to any circuitry in "the second set of electronics" then you (most probably) need to protect this electronics against ESD.
Usually the datasheet and the application notes of the devices used in "the second set of electronics" tell you how to treat them.
The datasheets also tell you whether you need to install EMI filters or not.
2) undamped LC or PI filters may cause resonances. Maybe this makes pp-noise higher than before.
For a reliable device I recommend to follow datasheet recommendations, and at least install some protection against overvoltage spikes.
3) I don`t memorize this. What about an internet search "USB ID function"?
Klaus