I used my 11 tooth cog quite a bit with the 52 front on my 42 mile ride I just finished. I wouldn't call it useless unless you are just saying it's useless to you.

As for the OP going to 11 speeds on the rear, yes they can, but they'll have to get 11 speed shifters which tend to be the expensive part of a component upgrade. Probably a new hub or entire new wheel too. Along with all the stuff that goes in between. Depending on the OP's terrain and how they ride, it might be better to just stay 3 x 9.

I'm of the opinion Shimano quit offering 3 x 11 stuff when they realized it was just too problematic, or had the potential to be on some bikes. 2 x 11 works well for me with a 52/36 in my terrain. But I only have low rolling hills and no really long climbs.