Forgive the obvious question, but are you absolutely sure you didn't accidentally have your own active sensors on, or shields activated? Both would be picked up by EM sensors, and be unaffected by speed changes.
The answer to question 1 though is yes. a maximum size, maximum tech thermal sensor has a strength of 3750 I believe. So it does depend on how advanced you think think the aliens are, and how much space they have devoted to sensors.