In English you "wear" both shoes and clothes. In Hebrew, you wouldn't say "לובש" for shoes, just like you wouldn't say "I eat water" in English (or Hebrew, for that matter). There's just another word for it.
Yes, it may be the plural of נַעֲלֶה superior, lofty. Biblical Hebrew also still had a (true) plural of shoe, i.e. נְעָלִים (beside נְעָלוֹת). But modern Hebrew has lost this contrast of dual and plural.