The only trains (so far) that will be "redirected" into and out of Penn Station during the convention above it are the "Midtown Direct" service trains of NJ Transit. These will go to Hoboken instead of Penn (riders will have to take either PATH trains into Manhattan, or use the ferry - which is what they did before the Midtown Direct service started).
Amtrak and Long Island Rail Road trains will continue to operate into Penn, and (at this point) I believe the NJ Rail trains from Trenton and the North Jersey Coast line will, as well.
Supposedly inbound trains will be "searched" - presumably by bomb-sniffing dogs, etc - before entering Penn. We'll see.
With the disruptions to both downtown Boston (North Station) and New York City (Penn Station), I feel confident in predicting that these two conventions are _the last_ major political conventions that will be held within crowded city centers. As they are now deemed "Special Security Events", they are just too security-intensive and too disruptive to the normal day-to-day activities of urban centers to be conducted within them in the future.
But both conventions are going to cause horrendous upheavals to the lives of "regular" folks.The one in Boston is the worst of the two,but yes,this will probably be the last political conventions in such large,crowded places.The security is a nightmare for ALL concerned.