I am aware that by default beacons are not allowed but even when checked to allow them in mod settings they still don't allow them.

EDIT: Sorry for the unnecessary post, turns out i actually didn't check that button.

EDIT 2: Turns out the problem actually does continue as the beacons don't affect the deep core mining drill.

Hello,

After a quick test it seems that indeed deep core mining drills can't be affected by beacon speed module effect. The energy efficiency effect work properly from the beacon however ! And you can't put productivity in beacons anyway nor in the deep core drills.

This must be because the speed and productivity effects are removed from the appliabled effects on the drills as intended to prevent them being overpowered.

I guess I could remove the beacon auto remove feature to lighten the mod now but then it might not be clear why speed module in beacon doesn't affect the drills (appart from the fact that you can't put speed modules in the drill itself, thus telling it is not allowed what ever the source).

Yes, this is how machines work. Either they can utilize the effect (speed, productivity, efficiency, pollution) or they can't and beacons respect that. Productivity modules are a bit weird because they're also checked on a per-recipe basis.