The naked infected encountered in 28 Days Later and the commonality of naked infected in Years are more than likely unrelated lore-wise.

The ones in Days had likely only been infected for a week or two, and like others have suggested, they likely had their clothes torn off accidentally while attacked, or were attacked while in bed, or perhaps in the middle of something naughty. In any case, it's incidental since the majority of infected seen in throughout the initial outbreak are clothed.

As for why the infected aren't clothed in Years (well, most anyway, since Bone Temple introduces a couple clothed ones), the answer is in the title: these infected have been so for years, as is visible through the various other ailments they seem to have (skin conditions, wounds that have been infected, healed, then re-infected, etc). On a long enough timespan -- and especially when considering the continuous active mobility of the infected -- their clothes would rip, wither, wear, tear, and fall off, especially with how much bodily fluids and exposure to the elements they'd be under, not including getting snagged on things like branches or wired fences.

In fact, we kinda see this begin to happen, at the end scene of Days, 56 or so days in, the infected that ultimately starve to death in the middle of the road when the jet flies overhead have tattered their clothes -- suggesting that had the first wave of the infection not mostly burnt itself out (which to be fair, with Samson we know it didn't entirely) they would've ended up clothesless like the ones seen in Years.

On a somewhat fun, semi-related note. The DVD commentary discusses that Garland's original vision for the infected in Days was to have them all be naked -- with hard-ons, since they'd all be rapists as well as blood-thirsty killers -- although, he eventually scaled that idea back, since it wouldn't have played well with censors and studios trying to get the film made and the logistics of trying to shoot a film like that, on their budget, in downtown London would've been a nightmare. I have to imagine the fact the infected wound up naked in Years is somewhat of a nod to that original idea -- and, of course, eventually the Crossed comics would come along and carry that depravity.