yes, you should turn off Smart Entry & Smart Start if the car is to be sitting unused for a while. If SE&SS is on, the fob should be at least 16 feet away from the Prius, or else both the car's 12v auxilliary battery and the keyfob's battery will be drained quickly.
I'm not surprised if your shop has had to jumpstart the 12v accessory battery with it kept in this state. You may find in the future that your 12v battery will not have quite the longevity (ability to leave the car unused for several days without needing a jumpstart when you get back).
Like on any car, the Prius has a 12v accessory battery, that can get drained down through parasitic loads with the car off sitting unused for a long time, or if you leave your headlights or dome light on overnight, or... Then the next time you use the car you'd need to jumpstart/boost it.
However, unlike on other cars, the Prius' 12v battery doesn't actually start the engine. It just powers up the computers, which then flip a relay making the hybrid traction battery active, and it's the hybrid traction battery that actually starts the gasoline engine through one of the motor/generators.
Procedure to jumpstart your Prius is listed in the Owner's Manual.
