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Can Sniper-like models (having the ability to choose a specific target) engage transported models in open topped vehicles, such as in ork battle wagons, if they have LOS to the model?

No.
Embarked models are not on (technically) the table.

No. The only model that could even possibly have any chance is the Vindicare assassin, but even that is shakey.

Thanks for the replies.

It's a no, even with the Assassin. As the second poster stated, the model is not on the board, it's just counted as being there for firing purposes.

I don't think you've been able to do this since 1st ed (there was a rules mechanic to do this back then).

It certainly wasn't in 3rd ed or later, but I don't have my 2nd ed rules anymore (just a couple of codices).

Even for a Vindicare, it's sitll no because they're embarked.
Sniper can pickindividual models in squads but you'd be targetting a vehicle.

You can't target a unit in a transport with a shooting attack. If you read the rules for embarkation, you don't actually put the models on top of one another. You remove the infantry models from the table.