I think you should always use the highest level abstraction easily available. If your data is geospatial, then use geospatial objects.
But be careful. Mysql is the worst geospatial database there is. Its OK for points but all its polygon functions are completely broken – they change the polygon to its bounding rectangle and then do the answer on that.
The worst example that hit me is that if you have a polygon representing Japan and you ask what places are in Japan, Vladivostok gets into the list!
Oracle and PostGIS don’t have this problem. I expect MSSQL doesn’t and any Java database using JTS as its engine doesn’t. Geospatial Good. MySQL Geospatial Bad.
Just read here How do you use MySQL spatial queries to find all records in X radius? that its fixed in 5.6.1.
Hoorah!