deprecated usually means "replaced by something newer".
Why is certain software deprecated? Many reasons.
1. Sometimes the original developer(s) just get tired of supporting and coding for something.
2. Sometimes they pass away.
3. Probably the main reason, is somebody comes along with something that works better and more reliably.
4. In some cases it doesn't always work "better" it's easier for everyone to standardize on.
5. Sometimes it's popularity, no one wants to write software that no one uses.
6. Much of Linux is going through some transitions today, gcc was the defacto standard
for compiling the Linux kernel and just about the all the binaries for many years. But the kernel as
well as more and more packages are now moving to be LLVM/Clang compatible. (Many are without
any changes at all)
7. In the case Xorg-X11, it just too big and cumbersome with too many pieces and too many developers working on too many parts, they weren't always aligned on where they wanted to go as
a group. Xorg-X11 is currently over 50 libraries or so. Wayland is more unified.
8. In some cases, it is distro specific by design. Example apt for Debian/Ubuntu dnf for Redhat/Fedora
9. In some cases it's due to security concerns by a security review board.
10. In many cases, the drivers for a specific hardware are no longer supported because hardly anyone uses that hardware anymore. Sometimes they are still around as "legacy" software.
Most of the larger distro's have reviews board that periodically add or remove some packages
based on the criteria above.
I'm sure there are more reason than I have here.