In my data folder many files, like textures and meshes, are in .bsa format instead of being simple folders. I have much experience with mods and I found this problem out when I tried to install one. I used to have many patches istalled but I had to change my hard disk since my old one was damages by power, so now I just have oblivion installed.
The BSA files are archives of loose files. Vanilla Oblivion stores them that way. Many mods come with BSA files containing their meshes, texture, sound, etc., as that cuts clutter. It has been discussed that the BSA should be the standard for mod files but it is not widely adopted.
When adding mods and patches, you can expect a mix of BSA files and loose files (files that are in data\meshes, data\textures, etc). So this is normal.