I use query many times a day, and for many reasons - tracking events, gifts, constituents, etc. It is a hassle to search for a query and not find it only to realize I missed a box that was still on an old setting - filtered to the type I used a few hours ago or in a different category. It's just a small thing that seems easy to change.
I don't know why the boxes are easy to miss for me, but when you open the search function in database view, all of the fields are cleared so you are doing a new search each time. I wouldn't expect that I am still working within the old filters as before. I very rarely need to use the same query each time I am in the query function, so having the filters static causes me more clicks.