I have always said..there are no stupid questions just stupid answers. So with that said Let me say this about this question.
I have travelled the USA my whole life and have visited thousands of churches. Not even the same denominations, yet I have yet to come across one that was practicing nudity.
The term: "Apparently", raises a red flag for me as well. Based on that statement I assume you have not personally experienced any of these churches that practice this ritual?
I also happen to notice you must have been talking about this a few times with people. Since you state "Some" and later go on to say "others".
My question , before answering this biblically would be why do you need to solve this riddle? What is it about this subject interests or disturbs you? Is it the interest in the subject matter? Or the rebuke for those practicing this wrongly? Or perhaps just a question to balance out your overall perspective on all things? Perhaps even to get this room talking about something? Only you can answer that. And I don't preclude which one it is.
I have to personally say, however, that I am glad God chose to use principles as well as specific commands, for if I had to read or one of the writers of scripture had to specifically state "And , if you attend church make sure you keep your pants on, for to not do this is wrong", ... not only would make my Bible be larger than I could read in a lifetime, but the writers would run out of papyrus.
Also, as you ask that question the issue of sexuality is brought to the forefront. Questions are fine, as I said, yet anytime we act in public our acts affect our surroundings, just a matter of fact.. This is a good and bad principle of truth. But I am just afraid Satan now can take a weaker Christian and let his mind wander unduly.
Now the answer Biblically. .... It comes from an obvious spot. The Garden of Eden. Gods intentions were that we would not need be embarrassed or misled in thought over nakedness, trust between God and ourselves had yet been broken.. Yet, the half- truth of Satan influenced the well known response of Eve showing her the hidden truth she was feeling robbed of, yet it was the awareness of her sin. as you probably already know she immediately was embarrassed and hid from God in her shame.
From that point now, nakedness is seen differently. It now is inappropriate, especially in the format of worship.We can say well we see it as God intended. But I see movements that have said the same thing..Harracritshnas [spelt wrong I'm sure, never cared to learn the correct spelling]..and many other cults that practice open nakedness under the ideology of it is pure, that ends up not practicing purity in Christ.
Satan wants "diversions"...this is one. We cannot escape sinful natures existence so why try?
Also, scripture answers this in many other ways..I can give you more specifics if you want to talk private. But just remember God says to go to Him over all things and do not be anxious about anything. But in all things in prayer and petition with thanksgiving- percent your requests to God. And the peace of God, that transcends all understanding will guard your hearts and minds thru Christ Jesus. Philippians 4:6-7.