With this mod enabled the ore deposits basically evaporate into nothing, disappearing completely after about 30 seconds, while the output is limited depending on the belt speed.

That is a base game bug fixed in 0.17. To compensate you can use productivity modules, which are bugged the other way around ;).

What do you mean by bugged the other way around?

Took another look and when mining to belts the effect is so bad i decided to make drills normal speed until 0.17.
I mean you get way more productivity than you should be getting. By a factor of a thousand or so.