I have some restored faith in your mechanic, then. Of course, keep in mind, too, that any shop is going to want to provide the most sound and comprehensive solution. This means using "quality" parts and possibly an "over-solution" so that they don't wind up redoing any work, either from a prematurely-failing part, or lack of solving the original problem with a lesser solution and having to eat any new costs (or worse, passing those costs to you).
Cheaper isn't always better of course. But then again, maybe it's not far from it. I can't attest to the quality of aftermarket cats, but when I see OE parts costing 3x-4x that of aftermarket parts (and we're talking several hundreds of dollars when it comes to cats and O2 sensors), it'll be a cold day in hell when I pay that amount without any certainty that said 3x-4x part will last 3x-4x longer. I only use OE parts if I absolutely must...and I rarely reach that point. But that's just me. Don't forget there's an entire industry also devoted to used parts, which is sometimes the best way to get OE-quality parts and aftermarket prices, if you don't mind some possible wear-and-tear.
As SMJ hinted on, P0420/P0430 can be misleading since it relies on other components and assumptions. Per the Factory Service Manual (
http://www.nicoclub.com/FSM/Pathfinder/2004_Pathfinder/, see EC-334), replacing the cats is the last diagnostic decision, after several prior steps before that have returned positive. That list includes an upstream exhaust leak...which you'd be surprised is actually not too uncommon. SMJ hits the nail on the head, too, by saying that if you have those code and any other codes (seemingly related or not), it's very possible that one is triggering the next. Beware the cascading codes! (And did the truck throw both codes? Each code pertains to a specific side of the engine, so if it's both, question the odds that both have failed, versus some other upstream component having a downstream impact.)
BTW, the FSM is your ultimate resource. If you have any inclination to do the work yourself, or a buddy who can help, that's the official Nissan guide, and it's very useful...far beyond any Haynes/Chilton guide. At worst case, it can help prepare you for any discussions with a mechanic. Best part: it's free courtesy of NICO.
Touching on the most notable issues you mentioned:
--Got me on the 'wub wub' sound...is it constant, speed related, happens during turns, bumps, acceleration, braking, etc.? Guessing wheel bearing at this point.
--The thumping on the drivers side...best guess, driver's side motor mount. Do you notice any sort of additional chassis pulse when it's shifting between 1st and 2nd gear under medium acceleration? A bad motor mount will cause the engine to lift when torqued, then the motor will settle back down. This is what was happening on my buddy's 02 R50 just last year...the mount had split in half. And you know the other part...we suspect it caused an exhaust leak on the driver's side, which then threw some codes (I'll have to confirm what they were). Changing the motor mounts are a PITA...fortunately we were working on a project that involved disconnecting the motor mount anyway, which is how we discovered it.
--Shudder during hard braking: excessive run-out on one or both front rotors. Limit is .10mm. Buddy's truck had this problem two months ago, too.
--Since the front tires are good, that's like a 50% discount on tires

. You can just replace the rears of course, though you'd want to make sure the sizes on all four are the same.
It's unfortunate that you're in this position, facing these sorts of repairs. But in all honesty, these are pretty straight-forward repairs and not atypical for this truck at this age. Personally, I wouldn't consider it a dud...it just needs some work, which I think is usually expected when buying used. But think about it this way: would you have spent $3K over book price on the same vehicle if you knew those parts had been addressed? Probably not; you just wished you had paid a little less knowing what you know now (yet on the flipside, if you paid $3K less, would it be harder to justify doing $3K of work?). That's just how I think about it...if you like the vehicle, and think it can do what you need for a little while, then it becomes an investment.
I can say this much, though: when the truck is in working order, it really is a solid truck.