I have just done the due diligence and actually contacted the MEP in question's office.
The spokesperson was able to confirm that this issue has been raised already and in the final text there will be explicit provisions that research and testing is still allowed.
Why pass such things? It's just another silly law to allow for applying another charge to someone during the arrest. In several cases you can see that the authorities slap on all kinds of charges in which most of them are eventually dropped. Kind like the throw pasts on the wall theory of law enforcement, something's bound to stick.
Plus it allows them to pick and choose who they arrest in any group when almost everyone in that group is possibly breaking a law they are not aware of.
That would be a useless law. For comparison: once murder is illegal, there is no need to have separate laws forbidding using a gun/screwdriver/BIC pen to kill somebody, is there?
Similarly, why would it make a difference whether someone usd hacking tools to commit a crime?
The spokesperson was able to confirm that this issue has been raised already and in the final text there will be explicit provisions that research and testing is still allowed.