I know of a lot of programs that once installed (or an update to the registry) they need something to refresh the values. This can be done by killing and restarting explorer.exe, however most of them do not do this and rather ask you to restart your computer. A process that takes a long time.
I'm currently writing a tool that will be used by technical people only, and it makes some changes to the registry that needs a reboot (or restart explorer.exe) to take effect. I don't have to worry about my users being freaked out by explorer.exe restarting on them so that's not an issue.
What else should I consider before doing this? Why do the other applications tell you to reboot instead of the faster, restart explorer? Is there a security reason? Or is it just habit?