"Where is the motorbike? Is it in the garage?"
Translation:Ble mae'r beic modur? Ydy e yn y garej?
The yn is not contracted because this is not the yn that connects a subject to a predicate (a verb, or a noun or adjective used predicatively); it's the yn that means "in" -- a different word that does not contract, though it is spelled the same.
yn mewn makes little sense, from what I understand; mewn is used for "in" with an indefinite noun (e.g. "in a shop") while yn is used for "in" with a definite noun (e.g. "in the shop").
And mewn isn't connected with the predicate-connecting yn, either.