To prevent drain clogs, I employ a few simple methods in ebb and flow systems:
1. Make your bottom drain fitting the pump outlet. This has the benefit of cleaning your drain screen and forcing growing roots back into the tray every fill cycle.
2. Keep the drain dry as much as possible. When the tray isn't draining, your drain should be dry. If you want a little water to remain in your tray, just install it slightly above the bottom of the tray.
3. Make the drain pipe a large diameter. There is a reason sinks and bathtubs have large drain holes.
4. Put a coarse screen that you can remove easily over the drain outlet. If the roots grow into the drain, simply remove the screen, cut the roots short, and replace the screen. If you have doubts about cutting roots, just move them far away from the screen and hope they won't find their way back in.
As you can see, my approach is one of improving the system design rather than applying patches. It's a pita at first, but once you work the bugs out, the effect is permanent. That way you don't spend your time maintaining bugs in your system and you have more time to focus on your growing. And then you can brag about what you did and how much better your system works.