They are both correct.
"The files are uploaded."
Uploaded here is used as a participial adjective. In this form, you are saying that once the files have reached a certain CONDITION, you will take action.
"The files have been uploaded."
Uploaded here is used as an adverb (although that may not be entirely true. My apologies in advance). The sentence, I believe, is in present perfect tense. "Been" is the verb that we must examine in this sentence. It stems from the word "be." "Uploaded" in this sentence serves as the CONDITION for the VERB "be." In this sentence you are saying, once our "be" reaches a certain condition, we shall take appropriate action.