2013 Prius C suspension and leak advice...

you can measure the brake linings yourself, pretty easy. they have warning noisemakers when replacement is needed.
ignore the leak, it's the timing chain cover, and a profit center for stealerships.
the suspension might need some work if it's bothering you, any unusual wear on the tyres?
it might just need new bushings

 

the pads probably aren't touching the discs. you would need to get a look on the same plane as the disc.
i'm not a suspension expert. you could take it to a shop that would make recommendations, and cost, then decide if you want to have a go on your own.

 

perhaps the stabilizer bar bushings?
suspension--suspension-components

 

I've changed the struts on a Gen 2 as well as a Gen 3 Prius. There are some differences with your C, but other than the rear struts, I don't think these will be all that different.

You're only at 90K miles. Unless you've got a serious problem that needs to be addressed, or you wait until the last instant before mashing the brake pedal for every red light, I wouldn't think you'd have that much wear on the brakes. Having the regenerative braking (which charges the high voltage battery) makes it so that you shouldn't need as much friction (normal) braking. My bet is just cycling through your brake fluid is all you'd need at 90K miles. I had to redo the rear brakes on my Gen 2 because of a small leak in the brake cylinder at just over 200K miles, and there was still plenty of friction material left on the rear as well as the front.

There may be a way of changing the brake fluid without, but really that normally takes a scantool that's capable of talking to the ABS computer, not just the main ECU. In the "old days," you could have someone pump the brake pedal while you open and close the bleeder valves at the wheels, but these days, that pisses off the ABS computer.

Changing the cabin filter doesn't even require any tools, so watch some YouTube videos (more than one because some of them may not offer the best repair strategy), and you'll save yourself over half of what the dealer wants by doing it yourself. It helps if you have a 10mm wrench or socket to change the engine air filter, but after that, it's the same thing (YouTube). You shouldn't pay a shop that much to change your engine air filter either.

Changing the struts is a bit more of a repair. It's a bit easier (and a lot safer) to replace the whole strut/spring assembly rather than changing just the strut part. If you decide to just change the strut part, a lot of auto parts stores will "loan" you a tool to compress the springs. There's no need to buy any specialty tool for the struts. After changing the struts, you should get an alignment. That's the only real specialty tool - the alignment rack. I'll pay for a shop to do that part (that and maybe changing out the brake fluid). After changing the front struts, you'll only be a bit out of alignment, so I've just driven the car a few miles to the alignment shop. That little bit isn't enough to mess up the tires. I wouldn't be driving the car all around town for a few months before getting the front end aligned

It's your car, so you get to decide what to do. For my car, if the front struts are failing, I wouldn't think the rear ones aren't that far behind. That's the one thing where your C may be different from the cars I've worked on. If the C is similar to the regular Prius, then the rear struts aren't inside the spring, and you can pretty much just change the strut. The Gen 2 and Gen 3 I've worked on didn't have a small access panels in the interior, so I had to remove the interior trim rear side panels just to get to the upper nuts. Again, watching a couple of YouTube videos to see what you'll have to do is the best plan. If your C has an access panel to get to the top of the rear strut, it would be a much easier repair.

For what they quoted you on changing the struts, you could pay for new struts all around for several cars, get the front ends aligned, and buy a scantool (at least the one I got).

If I read your original complaint, you heard a noise in the rear, and the shop diagnosed the suspension problems in the front. That doesn't make sense to me, so I'd start by having someone drive the car (10 mph or so) over a small bump while you stand off to the side. Maybe braking while they go by where you're standing in a flat parking lot, too. That way, you can hear where the noises are actually coming from and when. Are the noises coming from the front or the rear? Which side? When you go over a bump, or when you brake?