My house is he same way, built in late 90's, some of them are totally useless.
First I would pull some switches out and get a feel for the wiring. If it follows modern standards you should have hot and neutrals in the boxes with the feeds, and then then 3-way boxes may jut have the traveler wire and that's it. This setup gives you a good amount of flexibility.
If you want the best cost option, I would go with Zooz. You can replace only the main switch and leave the 3-way alone (may not even need to change wiring in some cases). One drawback is that you cannot usually pick which box gets the smart switch, it depends on where the hot feed comes in. The 3-way can then be used just like any other 3-way, to toggle on and off. You don't get the multi tap, etc... Personally now that everything is setup we hardly ever touch the switches themselves.
If you get into a bind and really need the smarts on the other end, you could also use the traveler wires to the 3-way to send a feed over to the box and wire in another smart switch. You then set up the 3-way control with associations or rules on the hub.
I would use dimmers everywhere possible. I even wish I had done dimmers on the outdoor lights, I may swap them out some day. A lot of mine I keep set at the same dim level all the time but then when cleaning or other certain activities I can ramp it up fully. Just keep in mind if you have cheap / non-dimming LED bulbs you might need to upgrade some to avoid flickering.
Check out the Zooz ZEN30, the relay should be able to handle the disposal. Or if you don't like that so much, then check out "Air Gap" switches for disposals. You could add the switch to your counter top, cabinet, or sink and then just wire it hot in the box up above.
Let me know if any other questions. I am a resident Zooz expert and also seem to have a similar situation as you with my house.
Oh and if you do want to go with Zooz, I have custom drivers for most devices, switches and dimmers are here: [DRIVER] Zooz ZEN Switches Advanced (and Dimmers) -- If you want to support my work there are affiliate links on my driver posts you can click to see the product pages and purchase direct from Zooz.
