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Sunburst is a Nova power. Does it affect units inside dedicated transports?

I've never really come across the situation before last night. Played against Orks, where there was Battlewagon and Trukk in range for a Sunburst.

My opponent and I both assumed no, it would not work against units inside the transport. Thought it might be a good idea to ask. Does open topped make a difference?

No.

Yeah, negative. Per the rulebook FAQ units embarked on transports don't interact with units on the table unless specifically allowed to.