I've rebuilt many an engine and have never heard of doing so in a clean room. I've also worked in many a clean room at semi-conductor plants, can't say i've seen that there...
But yes, you certainly want to be as clean as possible.
Well I said practically clean room
. I know the machinist is not going to be working in highly filtered air with a protective suit and gear to protect what is being assembled, but I have seen machine shops that have special assembly areas that are kept spotless, and that the cleaning of engine parts and protecting those parts after cleaning is done carefully. For instance all the oil galleys in the block and crankshaft need careful attention or it can shorten the life of the engine considerably. And after engine assembly, I have seen all is sealed carefully in plastic.