Yes, it matters.
Actually, it depends.
tar.gz
- Stores unix file attributes: uid, gid, permissions (most notably executable). The default may depend on your distribution, and can be toggled with options.
- Consolidates all files to be archived in one file (TAR: "Tape ARchive").
- Actual compression is done by GZIP, on the one .tar file
zip
- Stores MSDOS attributes. (Archive, Readonly, Hidden, System)
- Compresses each file individually, then consolidates the individually compressed files in one file
- Includes a file table at the end of the file
Because zip compresses the files individually, a zip-archive will most-likely have a larger size (especially with many smaller files - think config files).
So you see, appart from file size, if you zip a bunch of files on Linux/Unix, and then unzip them, the file-attributes will be gone (at the very least those not supported by MS-DOS - depends on what ZIP-software you use). This may matter, or it may not, in which case it doesn't matter (because the file-size difference is in most cases negligible).
Note:
Apparently, modern versions of ZIP also store Unix-file-attributes (depends on your ZIP-software), so with modern-zip-software, the file-size will be the only difference.