After Stormcloak Wins, are Thalmor Justiciar Still in Skyrim?

Yes

There are still multiple ways to encounter the Thalmor. Losing the civil war does not end the interest of the Aldmeri Dominion in Skyrim. it just changes things up a little.

1. Thalmor patrols hauling Stormcloaks to prison will no longer be present. Encountering the Thalmor in the field, however, is still possible, and they will now be hostile.
2. The Thalmor will no longer have a Markarth presence.
3. Ancano will remain in the College of Winterhold until you complete the Archmage quest there.
4. Thalmor will remain in the embassy, and may respawn, even after the main quest is complete
5. There is still a small chance that Thalmor will be found in the field in combat with people near shrines of Talos
6. The Thalmor prison at Northwatch Keep will become the new military base of operations for the Thalmor and will continue to spawn Thalmor. Imperial dialogue changes somewhat and it will become difficult to find out that Thorald Grey-Mane is being held there, as instead of giving details about the Keep, it will be considered "privileged information" and nobody will divulge the inner workings of the keep.

It's important to note that early in the Main Quest, you discover that the Aldmeri Dominion (i.e. Thalmor) doesn't care who wins the war; in fact, they want to make sure nobody does, so that when they are ready to aggress again, both Skyrim and Cyrodiil will be too weakened to fight back . A win for one side or the other just changes their tactics, but they are not the Empire, and so do not abandon their plans just because the war ended.

No

The Thalmor will still have the embassy. This is probably because of an oversight on Bethesda's part. They may have just forgot to take them out once the Stormcloaks won. OR it could be that they were allowed to keep the embassy, but loss control of the rest of Skyrim.

I checked into this by simply running over there and checking it out during the day. There are still Thalmor there.

EDIT

The Embassy is needed for the quest "Diplomatic Immunity", so that is why it stays populated.