If your going to consistently change out the water that often you might be okay with out running any bennies, but personally I would be preventative before reactive, i missed out on that one part of the nute recipe (actually just hadn't arrived in the mail yet and was anxious so started without hydroguard) running RO water and was slimed I think within 48-72 hours.
I'm now messing around with different mixes in my cloner half RO half tap water, with or without the hydroguard, rinsing with bleach water between res changes vs just rinsing with tap water, ( I have a belief that if I rinse the cloner with a bleach solution it would just kill the bennies in the hydroguard) I actually just finished changing my water in my cloner/seedling bucket (ez clone sprayers) before typing this, checked my ph and it was 8! With little seedlings in there that's a no go.... washed with bleach solution and rinsed throughly then did a gallon of tap and a gallon of RO and ph'd down to 6.5. We will see how it looks after a few days now with no hydroguard in the cloner bucket.
As far as tour hydroton I have never actually used it but my closest buddy runs flood and drain tables with them and I have also read a lot on here that if not properly rinsed and cleaned and soaked in ph'd water that YES the hydroton I fact can cause ph swings.
Was that brand new hydroton when you started or have you used it in a previous grow? Also did you wash it throughly? Heard it will also run off redish water until throughly cleansed.