The drivetrain spins the electromechanical motor at all times, adding drag. The drag is not just from the added mass of rotation, but also a dynamic resistance caused by electrical properties of the motor being varied in different ways so that the computer can achieve either regeneration (by temporarily changing modes to allow the motor and circuitry to act as a generator, usually during a coast downhill or to a stop), or additional braking (by electrically braking the motor, using the energy stored in the batteries, to add further resistance to the drive train at the cost of heat generation and range reduction).
If a check engine light that has to do with the electromechanical subgroups of your prius comes on (indicating a fault) those systems are disabled, meaning that the car is more or less non-hybrid during those times. Braking will feel stiff, and the car sluggish, but it is by no means dangerous to drive (unless you consider the new learning curve for the cars' performance profile to be dangerous, which it is.)
Also : Your emergency brake is indeed fully mechanical, but on newer models they may be released electromechanically via a command, i'm unsure. I haven't worked on one since the second generation.
p.s. you forgot a sub group. Your steering rack is also electromechanical. One of the first of its' kind in production. Meaning, if you ever experienced a total blackout, your steering would, too, become much more resistant. This , however, isn't considered to be a safety hazard, because at speed the steering rack does little to assist the driver. the forward momentum takes care of that. The steering assistance is mostly there for parking lot situations.
(source : I was at one time a toyota technician, and my back still remembers the recall on first generation prius battery packs, they weighed 124lbs and were way awkward to remove.)
All of these functions are electronic on the Prius (and indeed on every hybrid car that I know of that's on the roads). The balance between regenerative and regular friction braking in particular requires quite a bit of computer code and calibration to get right.
The point is, most of the options you've listed there really may be computer-mediated in modern cars. (And yes, I've heard that there's a strong correlation between unintended acceleration and older drivers, and that a lot of those cases really are driver error. But I don't think you're making that case here.)