I'm using Zelda Classic v2.50.2-win and Win10 Pro 64bit.
But I found out, what the problem was. It wasn't the game, it was the VLC player. Maybe hardware acceleration?
Without running VLC: 37-43/60 FPS
If VLC is running: 60/60 FPS
If someone else has a problem with a fast Link: Press F1 or turn off the VLC player.