Since there are more and more jailbreaks being created by hobbyists, each with their own respective quirks, you may have to change the behavior of your tweak / packaging depending on the jailbreak installed on the user's device.
None of this advice is foolproof but it's worth taking into consideration.
Electra (11.1.2)
/.electra_installed in the filesystem.
Electra (11.3.1)
/.electra_installed in the filesystem.
th0r
/.bootstrapped_Th0r in the filesystem.
unc0ver
/.installed_unc0ver in the filesystem.