The fixer-upper my husband and I bought is being renovated by a licensed and insured general contractor. 3/4" red oak site-finished floors were being installed in the living room, kitchen, and dining room yesterday by a subcontractor and I met my friend at the house so she could see progress (she loves house renovation stuff). She mentions that it looks like I have particle board subfloor, and that nailing hardwoods to it should be a big no-no.

So I go online this morning and the internet is in resounding agreement- particle board subfloor is BAD for nail-in wood floors. So I call my contractor in a panic at 7 am. He states that we have multiple layers of flooring, and that while particle board is the top later, plywood is underneath it. When he met with the subcontractor they discussed this and the subcontractor said that they will be using extra long nails to grip the plywood underneath and would be using twice as many nails as normal. He also stated that because we're doing wall to wall in multiple rooms and it will be getting three top coats there wouldn't be any problems at all with the floor moving.

I let my contractor know how unhappy I was that we weren't notified that they were installing floors specifically on a subfloor the manufacturer does not recommend. He stated that our kitchen cabinets are on top of the particle board and that it would be thousands of dollars and a rip-out of our kitchen to replace them and he felt confident in the subcontractor's abilities, so he didn't say anything to us. I let him know this was NOT okay, told him we are to be notified on any other issues so that we can decide how to proceed, and asked him to provide a written warranty on the floors for many years past the standard warranty he provides. At this point 80% of the floors are in and we don't really have any other options.

I guess my questions are this: could any potential problems with the top layer of the subfloor being particle board be mitigated by using extra long nails to reach the plywood, using twice as many nails, and the fact that it's wall to wall flooring on all of the main level? How long should I ask for the warranty? An extra 5 years?

Particle board will hold nails and be stable unless it gets flooded. When it gets saturated with water it will swell. Nailing with longer nails can make a difference depending on the thickness of the particle board.
It seems like you have only an underlayment instead of a particle board sub-floor.
An extra year warrantee would be a good solution.

I am installing nail down floors as well. My subfloor is all 3/4 osb, amd it is more than good enough for what I am doing. One thing a good builder I talked to did mention to me, is that if you have osb, particle board, or heck, even plywood, it's actually a bit of extra security to give your subfloor a heavy coat of Kilz primer prior to laying your moisture barrier. It just seals the surface of the subfloor a little better to prevent the issues you may be concerned with if it should ever get wet.