Yes... you have a good eye for ambiguity! This sentence could also mean: "The pens are not on your table."
Desk is table, frame, or case, usually with sloping top, but often with flat top, for the use writers and readers. It often has a drawer or repository underneath
"Masa" means table and "sehpa" means coffee table which is long, low table, often placed before seating in a living room, on which drinks may be served, and magazines etc placed.
The exact translation of ''Masa'' is ''Table'',''Desk'' is more like a smaller table,but it can be used I think,I am not quite sure.