Saurik has updated Cydia substrate to version 0.9.6300 which resolves Cycript not working properly on iOS 9.3 devices.
As per Saurik,
“Cydia Substrate 0.9.6300 enables Cycript to work in the way one would truly expect on iOS 9.3.”
Cydia Substrate is an essential package for jailbreakers, hence you should install the latest Cydia Substrate 0.9.6300 on your jailbroken iPhone, iPad.
How To Install the Updated Cydia Substrate On Your iPhone, iPad
Launch Cydia and open the Changes tab.
Tap on the Refresh button to update all of your Cydia repository sources.
You will find Cydia Substrate update under the Upgrades section.
Tap on Confirm button.
You will be able to install the updated Cydia Substrate.
You can install the latest Cydia Substrate on your iPhone, iPad as .deb files also.
Download Link To Cydia Substrate On iPhone, iPad
Download Cydia Substrate deb.
How To Install .deb Files On iPhone, iPad
You must have a jailbroken device. Guide to Jailbreak iOS 9.3.3/iOS 9.3.2 on iPhone, iPad and iPod Touch.
Download iFile app on your jailbroken iPhone, iPad by searching on Cydia.
Install .deb Files On iPhone, iPad
Download Safari Download Manager in Cydia to download .deb files directly on your iPhone, iPad.
Launch Safari app from your iPhone, iPad
Search for websites where you can download .deb files. Select to download .deb file
Tap on it and select Open in choose iFile.
Tap on Installer to install the .deb file.
Restart your iPhone, iPad now.
This is how you can install .deb files on iPhone, iPad without using Cydia.