Is it ok to put only 2 10' Component subs in a box that is already cut out for 3? Will it make it sound any different? Should I try and cover the third cutout up?
You'll definitely want to cover the unused hole but there's no way to tell what the affect will be until you try it. There are a lot of factors that come into play but generally speaking, a larger box will provide better low end extension at the expense of sound pressure. So in the end, that means your subs should sound really good on low notes but they won't be heard very far away.
The best thing to cover it with is a piece of MDF (or plywood) cut the same size as the outside dimension of one of your speakers. You can use one of your subs as a template to pre drill mounting holes in the plug so that your screw holes will not be outside the speaker mounting area of the baffle.