Is he the same John B. Howe who applied for a TX Confederate pension from Wilson Co, TX?
On the GNIS site, I do not see a Magnolia Cemetery for Lavaca or Wilson Co, TX.But, there are half a dozen cemeteries named Magnolia on that site.Not every cemetery makes it to their list.And, it's not uncommon for older cemeteries to have a name change, or two, along the way.
You might post queries on both the GenWeb and GenForum sites for both Wilson and Lavaca Co, TX, ask if anyone knows of a cemetery that is, or was, named Magnolia in their county. Happy Hunting. (^_^)