Just bought a 2006 Jazz with the same problem. Personally, I think drilling holes might drain the water out, but it's also another way for the water to get in.
After looking at lots of Youtube posts, I traced the issue to cracks in the sealing putty between the rear side and boot panels (near the boot hinges). I've cut out the sealer with a dremel and filled the gaps with Araldite Steel 2-part epoxy. Photo attached shows the original crack.