Its clear (at least in the current version) that yellorium is extremly easy to come by, and if a pack has big reactors, than it is the go to powe option.
What if you would have an another item/ fluid after as actual nuclear waste?
-If fluid: if stored in regular tanks, than you get negative effects (maybe even some permanent ones)
-if item:if stored in regular containers, -||-
-I would say that it should be your own fliud/item code, so it can not be transferred into anything whitch would void it / somehow prevent it from being disposed at least in the known ways, so the player has to set up a place to store nuclear waste.(you have to ballance aganist possibilities outside your scope)
-The waste production could be dependent on:
-fule type: bluthonium produces more waste
-reactor size: larger size produces slightly more waste. (mostly for ballancing)
-ina 3x3x3 yellorium fueled reactor the waste should be insignificant (there should be some, but it should not vause issues).

I personally don't see the point of forcing the player to store such waste, as it would just end up being annoying more than a balancing point since space is way too easy of a thing to come by (who doesn't have a large quarry they emptied?). Really all that would do is encourage people not to use this mod at all (as who really wants to store tons of waste in a video game?). Instead, try balancing it using the configs, such as reducing the ore quantity, or reducing the fuel quality multiplier.

Also, there is really no way to force the player to store a liquid/item, as there is no easy to blacklist voiding on all liquid/item voiding things, and making a new "item" type just requires BigReactors to create their own containers simply to store the waste (and even then what is to stop the player from breaking the container to delete the contents? Or if it preserves the contents: throwing filled containers into lava/the void? Or if they are immune to both somehow: leaving them to despawn? Or if they don't despawn: leaving them in all in a pile out of the way to ignore?). Really making the waste impossible to destroy is more trouble than it's worth.