The friends who hadn't been wearing hats seemed to have red noses and cheeks.

Literal

Hat [object-を] wear-[past negative progressive-てなかった] friends [topic-は], nose [and-と] cheek [subject-が] red-becoming-[ようだ].

かぶる is the verb for wearing headgear (hats, helmets, wigs) — Japanese uses distinct verbs for different clothing: 着る for torso garments, 履く for footwear and legwear, 被る for headgear. ~てなかった is a casual contraction of ~ていなかった 'had not been doing/wasn't.' ~ようだ here indicates inferential 'seemed like, appeared to be,' based on visual evidence. ほっぺ is a casual/affectionate form of ほっぺた or 頬 'cheek.' The sentence describes a cold/winter scene from the speaker's perspective.