Here’s an American English answer — it could be both! But I would usually assume they were talking about a pen with blue ink, and since most pens with blue ink are also blue on the outside, this doesn’t come up very often. :)
An exception would be if there were a bunch of pens on a table, and some of them were blue. Then if someone said “Which pen do you want?” I could say “A blue pen!” without knowing the ink color. But overall, if someone were to ask me, “Do you have a blue pen?” or say “This blue pen is really beautiful,” I would think they were talking about a pen with blue ink.
One small note: I would never say “it’s blue pen,” I would say “it’s a blue pen.”
Hope this helps! :)