In the end of 3D when Xehanort summons the No Name keyblade Mickey says "oh no! Are you?" Does he mean that he found out about him being Xehanort or does he know the Unknown secret boss of BBS?

I don't think Mickey ever saw Young Xehanort in BBS, as he never mentioned him in any of the other games. Probably pure coincidence.

The reason Mickey said "Oh no. Are you?" is because he figured that young Xehanort was the one who was able to time travel as he and Yen Sid had speculated.

mickey realized youngxheanort had the power to time travel and had the power of master xehanort hince his eyes glowing gold and a dark blue and black aura around him while he summoned his keyblade for the first time

Edited December 2, 201212 yr by Khrulesbbs

Mickey put 2 and 2 together and realized who YMX was and how he got there...And, on top of that ,he realized MX transfered his consciousness to YX's body and had YX summon his keyblade and fight ( Although it was really MX fighting in YX's body.)

Edited December 2, 201212 yr by Flaming Lea

In the end of 3D when Xehanort summons the No Name keyblade Mickey says "oh no! Are you?" Does he mean that he found out about him being Xehanort or does he know the Unknown secret boss of BBS?

 

Ok so different topics are known.

 

- Mickey thought that YX was Terra

- He figured(thought) that YX was the one able to walk through time without no body around

- Or he was just amazed that how Xehanort put his consciouness to other bodies, because afterall that was YX!