You are leaving the yellow tile? If you can't find matching tile or a coordinating decorative tile to use, I would look for a taller mirror and hang it so it covers the holes. I think unless you use a whole row or two of different tile that just two in those spots is going to look odd. You could space several of them the whole length of the vanity, or find a mosaic glass tile with yellow and black to try to tie it all together and put a few rows of that the whole length of the vanity. Or even take out the tile above the backsplash and use all granite to the mirror. But that's all going to look like a hodgepodge. I think your best bet is a bigger mirror.

I have 6 of the 4 inch LEDs in my roughly 14x14 kitchen with a 10 foot ceiling. We do have an island fixture, but those LEDs provide a lot of light. They were originally halogen, but we replaced the bulbs with the HD EcoSmart/Cree retrofit kit (includes the trim and rim). I haven't tried other LEDs but I understand these have a nice bright white light and are well though of compared to others. I'd make a trip to Home Depot and try one. Screw it into a bare lamp and try it in the room to see what you think 3 or 4 would do for you.

The difference between 6” and 4” is roughly about 200 lumens - 6” are typically around 900 lumens and 4” around 700. So between the three cans it’s a 600 lumens difference which amounts to roughly one 50W light bulb. I don’t think that’s a huge difference personally. We have a windowless bathroom a touch bigger than yours (9x8) and we’re doing five 4” cans, two over the shower (it’s long and narrow - 70” long) and three in the room plus two LED sconces. Right now we have four 6” retrofits and it’s pretty bright.

Some give out more light than others. I have this in my hall bath and it looks awesome and provides nice ambient light (perfect for guests) but it isn't good enough light to shave or put on makeup. Some have the lights facing forward and I expect they would be better for that use.