I think the sunglasses are more likely, to cover up the fact that he's not wearing eye makeup.

They can't be to cover up the fact that he's not wearing contacts. Because he almost always is, wearing his blue contacts. If you squint during most of those interviews, you can see that he's still got the blue contacts in, with the dark sunglasses.

We also know his vision is at least a bit off.
Because a few years back, he was talking about how he and You wear the same frames. He also said that You sometimes accidentally grabs his glasses and goes around stumbling into things because the prescription on Gackt's glasses are to weak.

So...yeah.

I became really suspicious of a light sensitive eye condition, around the time they started filming Furin Kazan, though.

Apparently, there was bit of a stink the first time they tried taking photo's of him as Kenshin. Its been a while since I read the article but if I remember correctly;
When they got him in costume, he refused to take pictures without his contacts in. So they had to cancel the shoot for the day.

Its true he did have brown eyes for most of the photo's and all of the series, but I'd bet he just went out and got himself brown tented contacts.

(oh, and lets not forget that rapid blinking, hes forever doing)

Or...maybe we're all reading way to much into it and he's just really likes those contacts. ;p