It depends. If you search for onion flower you will find a lot more information. Basically if you want seeds, let it flower. If you want to eat the onion/shallot cut it off. These will not store as well as a result of the flower that will be growing in the onion, some people say that it will have a weird taste, but I have never had a problem eating my onions that have flowered.

Here is a link that might be useful: Search For Onion Flower