The GTS checks all the Data for Shaymin such as the Moves, Ribbons, IV, EV, Met at Lv, Met at Location, Hex Values, ID No, PID and SID.
So if any of those are incorrect, you will not be able to trade over a Shaymin. Shaymin is not blocked at all and the only Pokémon that is blocked is Arceus.
I traded my Space Deoxys for a Shaymin on my SoulSilver that was caught in D/P/PL via GTS.