Some people keep filter material in their sumps, like a sponge, to grow enough bacteria to allow that to be the bio filter in an emergency QT. In a situation like yours yes ammonia will be a problem. You can use Seachem's Prime to help. But you still need to be prepared to do lots of water changes. Put some filter material in the QT anyway so after a couple weeks of water changes you will have some beneficial bacteria to help.
The reason not to put rocks in QT is usually for Cu treatments. The rock will absorb the Cu and become useless. The ich attachment to the rock is not a real big concern if you run the hypo long enough to break the life cycle. But hypo may also kill much of the beneficial meiofauna living in the rock. Mingo is right in that bare substrate will make it harder for the ich to attach. When you do your water changes to control NH3/4 siphon the bottom to get any recently released trophonts.
If you do hypo also be prepared to do top offs twice daily to keep your salinity from rising. Also watch your PH. It can really swing in hypo.