What's causing the knock/rattle over bumps?

I've gotten under it 3 times now (03 Honda Pilot) and can't find where it's coming from. ALL bushings appear to be intact, can't move links, sway bar, tie rods. Wheels do not tick, whine, squeal, squeak or pop when I turn them. Tried to bounce it from top AND from underneath, not a sound. But, when I go over bumps, most ones where the wheels have to drop, rather than rise, it knocks and rattles. Engine does not have excessive movement in gear. The only problem I found underneath was the Inner CV boots are leaking. I don't have a jack so I didn't and can't jack it up. Is it possible it's CV axles causing it?

That definitely sounds like worn shocks, or a broken engine mount.

Best fix te CV before it becomes more expensive. If it cures the noise then bonus.
Check for loose panels, mudguard inserts, look for moving, pivotting sliding places with dirt rubbed off.

I'd agree with fuzzy, fix the CV boots before damage occurs to the joints. Regarding the knocking, it sounds like a faulty shock to me but I'd want to hear it to be more certain. Have you tried waggling the exhaust?

Check the exhaust system. It's suspended with flexible insulators. One or more may be damaged or broken.

Your lug nut wrench is causing the noise from the back of the trunk.

Yes, it IS possible. Have them inspected by a PROFESSIONAL.

The only time I've had noise from CV joints is the knock… Knock… Knock that they will make going in tight circles under acceleration when they are bad.
You fail to tell us how many miles are on the vehicle.
You haven't even jacked the wheels off the ground so you obviously have no clue if the ball joints are worn.
You may have noise coming from the struts or even the stabilizer bar bushings.
Take it to a mechanic. You're not going to get find it at the rate you're going.

If you can't jack the vehicle up to test ALL the suspension & steering bushings, along with the engine, transmission, and exhaust mounts, then you can't eliminate them from causing the knock/rattle noise with just a visual inspection on the ground.
Some bushings, like the ones on the sway bar links, are pretty easy to see if they are worn, broke or missing, but others, like the rear lower control arms are difficult to see and impossible to tell if they're bad by just looking at them, even if the vehicle is on a lift.
Find a local trusted shop and tell them your concerns, then they can address the knock/rattle noise accurately.
Also, fix the inner CV boots. While it's not too likely (but not impossible) that the inner CV joints are causing your noise, when both inner CV boots are split & leaking, that's an indication of a bad rear engine or transmission mount, as excess engine movement will over stress those boots and cause them to split & leak.

Depending on the type of vehicle you are driving it could be your body mount bushings or your strut bushings need replacing. It will make a thumping or rattling sound especially if you hit a pothole or driving down rough roads.

As you can't jack the car up to take the load off the suspension, your visual checks are wholly inadequate.

The noise could be the CV joints but that's very unlikely, although you do need to test the joints for knocking before deciding how to repair them: find a large empty space and drive forward with the steering on hard lock and then reverse back on the same setting. Then repeat on opposite steering lock. Any knocking or clunking means you're too late to repair the leak and the joint will need replacing. For most Honda models that requires a complete driveshaft.

You can check one more thing you've not mentioned: the exhaust system. It could be that one or more of the hangers are weak/broken/absent and that allows movement which knocks against other parts.

If that isn't the cause then the car needs to go to a repair shop: better equipped ones these days not only have the usual vehicle lifts but also have shake-tables which simulate the car travelling over a very rough road. But even without those a good mechanic with a pry bar can quickly identify almost all causes in just a few minutes.