Having a flick through Auto Trader I noticed that some of the Tfsi engines had the cover on top of the air intake missing. Would this prove beneficial or cause issues?

From this

To this

Sent from my Galaxy S5

Mine looks like the top, never considered it to be a cover because the inlet is at the front. The bottom one looks more like it's had a hole cut in the top!

It would pull a tiny bit of warm air in.  The car might be a bit sluggish if the engine bay is really hot.

 

I doubt it would cause a problem as it still has to go through the filter