Hi Nasick,
There's no risk in deleting bex queries in the prod environment, provided you have enough authorizations.
People use to delete queries in which are no longer needed/ obsolete.
One important point you have to remember. There are some variables created for the characteristics in your infoprovider in the query designer which might be used in some other queries as well.
These variables won't let you delete the query due to references. You better have to delete those, before deleting the query.
My personal advice: If you don't need a query, I'd simply suggest you to remove it from the roles. In this way, your query will not be viewed in the bex analyzer or anywhere.
Save time and create a new query instead.
Br,
H