One of the issues was using iMessage and notifications were not being sent to me in many apps from Google Mail, Yahoo! Mail, to SnapChat and Instagram!
As for iMessage, it wasn't working as it should. Messages were not being sent through iMessage and while others were sending me messages, my iPhone was not converting iMessages into texts from others and receiving them. Instead, there was some sort of jam in the transmission that made Apple servers think my iPhone could receive iMessages but my iPhone really couldn't.
If you are facing either of these issues, I may just have the solution to fix your issue.
My particular issue appears to be in the Sources of Cydia. I'm not sure the exact details why, but what I did seems to have fixed the issue.
I removed all sources that I added to Cydia and left all the ones that came with the jailbreak. After doing so, I checked to make sure my apps from these sources were still available. They were and I rebooted my phone.
After rebooting and coming back to the home screen, my notifications icons returned and iMessages that were stuck in limbo came all at once. I was able to confirm that messages not only have their notification icons but also send their original ringtone and light up screen as before.
This makes me curious as to what sources actually do, what effects they have on our devices, and if having too many can be an issue or if it's just one or two that affected it.
If anyone can, can you explain any of these questions to us? I, in particular, am curious more about sources.