I'm guessing that some game betas would work and others will not... Since HDLoader doesn't work with every legit PS2 game out there, most games run perfectly, but there's a good chunk of ones that don't... So my guess is it would be the same way with debug code.
If a finished retail game works with HDLoader, then chances are its beta worked too... and if a certain game beta didn't work with HDLoader, then it likely (but not necessarily I guess) still wont work when it's finally released.
All just guessing on my part.