There are no automatic deletion of cache files, that I’m aware of. But, when packaging files like that and it’s a large project, it will take a while(Speeds vary depending on your system). For example, think of your GPU being used to compile shaders at it’s current version (GPU Software version 7.6 or something), if your GPU drivers update, it will recompile those shaders again. This also works this way with files you change inside of UE. When compiling/packaging if it sees files are out of date it will recompile all of them. This is intentional and will prevent corruption of your files. I hope that helps explain it to some degree.
dont delete your saved folder after you package first otherwise it will have to do everything from start again. Also check in your project settings/packagin you dont have Full rebuild ticked. lastly you could also precomile all your shaders to dcc with command, that should help
you can set default ddc folder in Engine settings and you can run fill command from cmd.
I only delete the “Cooked” folder inside the Saved folder after I package each time. Was that the one that I should have kept? But if I package the project right after I delete the Cooked folder, it still packages fast.