While there isn't much research I could find upon this,
Asking a question doesn't necessary act as a prompt.
While I would definitely agree on using the question more if you were to speak with a Voice Assistant such as Google Now, SiRi or Cortana; in a Windows application with straightforward prompts such as Click here to Start, I think it's natural to go with the command.
It would be completely out of context to ask Would you like to click here to Start?
You are essentially encouraging the user to click on a particular application (assuming there isn't a default one or there couldn't be a compatible one that could be located), so using a command for a quick action by the user is appropriate. By using a question, you are basically having the user think about it for a couple of seconds longer before selecting.
As far as actions which have options one can select without the use of a Voice Assistant are concerned, I would definitely recommend to stick to the Command since it is straight forward, conveys what you need to do and does not have the user think a lot.