Im curious what does substrate do? And can't it be updated later on the fly if we've already JB?
If Saurik updates Cydia, then yes, you should be able to update it. I have not done the jailbreak yet, so I am not certain if it was installed by the jailbreak. If it was, then you should get an update in Cydia. If not, then you might be able to install it via SSH if needed.
I don't think anyone here doubts that Saurik will update Cydia. From my jailbreak experiences, it seems that he gets an update out within days if not sooner.
If you don't know what substrate does, it has been covered many times on this forum. You should search the forums for it, for a better answer, but basically, Cydia Substrate, is what makes most JB hacks, tweak, etc possible to work. Occasionally, there might a tweak that conflicts with your combination of Cydia/IOS versions. Some of those conflicts can be fixed by Saurik, and the others can be fixed by the developer of the tweak. Sometimes, the developers don't/can't/won't fix their tweaks to be compatible.
An example is the ReachApp, I sent a message to the developer to let him know that the tweak prevented the Discover.app from functioning correctly. The next morning there was an update that fixed it. This developer fixed it right away, but I am sure that not all developers are the same. (He never responded to my email, but I am sure my email made him aware of the issue. It may have been a coincidence, but who knows?)