Boober's lack of eyes

[RedPiggy]

Well, other than just assuming he has really tiny eyes, there are fraggles with shorter hair (or little to no hair) that clearly have no eyes, unless it's like Bunsen, who technically has no eyes but we're just supposed to assume he does.

 

[TheRealFraggle]

Boober's puppet being made without eyes was clearly just a stylistic choice. The character must have them, since he isn't blind, so the obvious answer is that they're very small and hidden under his hat and hair.