The PVC tubing never gets plugged up. It's just too wide for that. I've only ever had one tub get a clogged up sipper and I just replaced the sipper valve and it worked great again. Also, if you ever do have a mouse escape the escapee is going to get thirsty and will chew right through the rubber tubing. That doesn't happen with the harder and thicker PVC tubing.
Important note::: I had someone contact me recently to let me know that the 3/8" holes in the ends of the PVC caps don't work anymore, you need to drill a 1/4" hole now. It looks like Ag Select has changed the style of their screw in sippers so that they're smaller in diameter. So PLEASE make sure that the sippers screw in tightly to the end caps BEFORE you cement everything together.