Can Android devices be used to clock in a RFID/HID timeclock for work using NFC? Using the software, I can register the cards with the timeclock. But would I be able to register phones?
Generally no, unfortunately Android phones can't be used as a card easily as phones running the stock OS can't emulate a card. This is due to restrictions put in place by the Android operating system rather than the underlying hardware. See also this and this where I've answered other similar questions.
Saying that it depends on what you're using as an RFID timeclock. If you were making your own then you could use Android's NFC peer-to-peer mode to talk to the clock. Another alternative is instead of using the stock Android OS is to use Cyanogenmod which does allow for emulating certain card types.