To directly answer your question- I would probably fix it and drive it for another 10 years to get the value out of it. I never put money into a car to sell it unless I had a lot of time and did the work myself. You could probably make the most out of parting it out if you have the location to let it sit while you are taking parts off it. Otherwise trade it in.
My opinion- the quote is consistent with what I have heard for a new part, but they are trying to sell you an easy parts swap rather than doing the diagnostics. The actuator problem is well-known, but I didn’t think it would throw the communications codes, so I am skeptical if all that happened at the same time. I would want to find the cause of the U communications codes and find out if the C codes could be caused by whatever set the U codes - maybe a bad brake ECU or just a corroded connector which resulted in the U codes. I would research what codes go along with the actuator problem. It was also not uncommon on the Prius of this generation, so that forum is also a good reference. For a while it was under extended warranty. Search for campaign ZG1. I recall reading that the problem is a small leak in the accumulator chamber. The fault occurs because the pump motor runs continuously to maintain pressure to keep up with the leak. The motor eventually wears out. Replacing the motor may keep it going for a while.
I understand that good used actuators are hard to find, but you may get lucky. Try car-parts.com.
For the air leak, you can probably find a good used air tube on car-parts.com. Check western states.

 

Help me think through options, given the inflated used car market. Should I repair and keep, trade as is, or possibly face massive loss with repair exceeding the value… Our 2006 Hybrid Highlander Limited is in otherwise good condition, at 153k miles. But my dashboard lit up with warnings a couple of weeks ago (ABS, brake, check engine, check VSC system).
Codes:
C1241 Low or High Power Supply Voltage
C1256 Accumulator Low Pressure Malfunction
C1391 Abnormal Leak in Accumulator
U0073 Control Module Communication Bus Off
U0123 Lost Communication with Yaw Rate Sensor Module
U0124 Lost Communication with Lateral Acceleration Sensor Module
U0126 Lost Comm with Steering Angle Sensor Module
U0293 Lost Comm with Hybrid Vehicle Control System

A broken air intake boot was found, but the part wasn’t readily available locally. We were told the “abs module has failed, cycling on and off-shorted internally.” Recommended replace abs module and pump assembly. Very high initial estimate ($3k+). Thoughts?

The choice is ultimate yours because you will have to live with the choice you make. You could spend $3000 to repair the ABS module and then have an hybrid system component fail due to the age of your Highlander which can also be costly to repair. Older car does require more money up front at one time to keep running as oppressed to making bite size car payments for years. Car payments can be budgeted and is a known expense that many owners are prepared for, but random repairs that can cost over $1000 can be tough to deal with at the wrong time.

I personally will not keep an old Hybrid due to the expensive of the battery and other hybrid components; let alone the normal wear items like ABS module, suspension, oil leaks,etc to deal with as the Highlander ages.

My vote would be to sell(trade) the Hybrid while you can as is and buy a used non-hybrid model.

With that being said; if you can repair your own Highlander then it maybe worth keeping since the ABS pump is not too hard to replace yourself if you can work on a car brake system.

The reason I did not buy a used Hybrid Highlander-The battery replacement cost and work needed to replace.

 

Can I use the Prius ABS in the Highlander Hybrid?