Can you fake a larger EM or cross-section? Could a small ship pretend to be a larger one?

Cross section would be harder to do; it's physical size. EM is definitely possible; lots of items have pools they fill up. EM is normally a multiplayer of how much is in those pools. If you emptied and filled those pools repeatedly, you'd look like you have a big pulsing EM. Same with heat. Shields and power plant are the biggest EM signatures. If you toggled them on and off, you'd be lit up in EM.