The short answer is yes, I do shim the coupler - you can see it in the picture below (I use a .06 thick styrene plastic piece)
But it should also be noted I lower the car by removing the piece the trucks ride on and replace it with my own concoction....it lowers the car by a good 1/16-1/8 of an inch.
I decided when I started in 1/29 that I needed a coupler height gage like I used in 'O' scale (my previous Model RR life) - this can also be seen in the picture below.
But, nobody makes one for 1/29.......so I made my own. I didn't want a 1/32 gage since it's height would be approx. 1/10 off.
I know my equipment will probably not mate up with others - if they use the Kadee gauge one height gage....that's ok, I probably won't use my stuff other than on my layout.