So basically they had no idea and no proof as to wether or not hamilton had an advantage.
...so they gave him a penalty anyway.
It just does your haed in, cos when ferrari broke the rules last time out (and I'd consider theirs as being more dangerous...ei. the pit lane thing..oh and they actually ran one of their own pit crew over too!) the stewards were considering a 10 place drop for the next race. Leaving them with the win that they had just achieved...but it ended up being a 10,000 fine for massa.
They should have said 'yes, hamilton gained an advantage so we'll give him a 10 or 5 place drop for the next grid'. It would have attracted a lot less attention to the corruptness of the penalty system.