I really liked Retrograde as well. Not exactly a standard shooter, but probably fits in the category still. C64 Rtype I enjoyed, even if it is a little different to the arcade/amiga version (loved it in the arcades and was pretty happy with the amiga port). Katakis is a great game, better than the official Rtype port. Armalyte I really liked too. It's a shame the amiga version isnt just a straight port with enhanced gfx, as while it looks nice enough it's a pretty average game at best. One of my favorite c64 shooters though was iO. Was the 1st game I bought rather than trading with friends at school. Graphics are on par with those of Armalyte in my opinion, an was released beforehand. It never got the attention it deserved, again, in my opinion. Forgotten Worlds I quite enoyed on C64 as well, and was another game that I bought (they were few and far between when I was an adolescant/early teen).
So, yes, as the topic suggests, I guess the c64 did have lots of good shooters
These are just the ones I played more than others, and without having been particularly a fan of genre (not to say I disliked it though).
One game I would love to see though is MetalDust. I've seen some videos on you tube and it looks very impressive. Resolution and color palette aside the graphics effects are as impressive as any amiga shooter I've played with multi layer full screen parallax, near full screen enemies, animated backgrounds, etc. Unfortunately SCPU's arent common, nor cheap (and required for MetalDust)
Maybe one day