I think some shoes are just worse than others. I have a pair of Northwave boots that suffer from the catpiss smell while all my other boots/shoes are generally ok. I wondered if it was perhaps something to do with the materials used or even the glue used.
I’ve had a few shoes develop a more musty smell, usually after they’ve been through a bog or other “organic” wetness. Trainer spray sometimes works, but I’ve also taken to completely soaking and washing them I something like Milton’s or Puriclean.
The Maxxdry linked above is also excellent. With a constant stream of wet biking, running and walking shoes over the winter, we’d not be without one now.