A new follow-up to this issue.
After doing yet another test upgrade to solve some other problems, I ran to this issue again.
I tried emptying OJS cache and also tested the solution Vitaliy described, but nothing worked.
However, this morning I opened the site with another computer and everything worked. So, it turned out that it was the browser cache that was causing the problem. I do not know what was in the cache, but it was maybe coming from the old OJS2 installation in the same address and was somehow messing things up in OJ3. After deleting my browser cache all javascript is loading.