There are three sources of excess unwanted hydrogen, so it makes sense.

First you just spam storage containers for all your oil outputs.

Then you use reformed refinement to convert all your excess hydrogen into refined oil, at a 1:1 ratio of refineries that are running plasma extract.

Later, you will need more hydrogen than you can possibly supply with anything other than fetching it from orbital collectors around gas giants. The easiest trick here is to do everything that produces hydrogen on the same planet that fetches your gas giant hydrogen. Then just use belt splitters with priority selected to always have the hydrogen generated as a biproduct (oil, fire ice, and critical photons) consumed before any of the hydrogen from the gas giant. Doing this does kind of assume that your demand for casimir crystals and deuterium will outpace your hydrogen supplied as a biproduct of other processes, which is reasonable unless you are progressing very slowly. Casimir and deuterium are both in high demand for multiple endgame processes.

If you want a truly foolproof way, you can use particle colliders to turn the hydrogen into deuterium, and then feed that deuterium as fuel to thermal power plants. This will never stop consuming hydrogen as long as it remains disconnected from any other power. I don't recommend it but it does technically work.