I’m not convinced the number affected is as large as 6000. Most of the PPLs and LAPLs I come across flying EASA aircraft at the clubs I instruct at have at least a LAPL medical. Those flying Annex 1 aircraft as owners are much more likely to have gone down this route, and so would not be directly affected – it wouldn’t stop them taking their 1 hour dual instruction or even a proficiency check for SEP revalidation in an EASA aircraft at a flight school/club since you don’t require a medical for that. It is also unclear if this includes the many microlight pilots flying on NPPL(M) licences.
This is just a symptom of the very poor data that the CAA publishes about the number of pilots, licences and medicals they oversee. It would require some “de-duplication” analysis between licences, ratings and medicals issued to determine the number of potentially active pilots affected. The difficulty is that since the PMD does not need to be renewed online until age 70 (unlike the FAA Basic Med every three years), it is very difficult to track or assess how many LAPL licence holders have dropped out of flying and are no longer current.
Nonetheless, I could believe this will affect a number of pilots who will not be aware of the problem if the derogation isn’t extended, and will simply carry on flying. While I don’t believe this has any impact on flight safety, it may have implications for any insurance claim since the pilot would not be flying legally. However, even then, I’ve read in the past that in many cases the insurance companies would still pay out to affected parties.