If it's something with the Update.esm, then would I be safe if my mod doesn't use that? Because, again, since getting the beta patch on Thursday I've put at least 20 hours into the CK and my mod doesn't CTD or fail to load or get any issues anywhere.
I am not an expert on this, but:
If "my mod doesn't use that" means, that when you created your mod, you did not have update.esm checked in the CK, in which case it would also not be a required master file for your mod, my
guess would be, that you might be ok. Or you might just be lucky, I really don't know.
However, update.esm contains Bethesda's fixes, and if that is not included as a master when creating your mod, and your mod modifies a record that has also been modified by update.esm, then your mod will be based on the purest vanilla game version, and will not contain whatever fix Bethesda did to that record. If update.esm is checked as a master, then your mod will be created as a further modification of the record in question, starting from how it was in update.esm, and Bethesda's fix will also be included in your mod. So, as a side effect, you may lose some fixes made by Bethesda. Still, update.esm has not had very many fixes in it so far, so that loss may not be significant.
(However, any early mods, even if they have been created with update.esm as a master, I think, are likely to miss out on later Bethesda fixes, if those are made to the same records that are contained in the mod and therefore "frozen in time" so to speak. It will be interesting to see how that will turn out.)
(Also, if a Bethesda fix makes complementary changes in two different records, and a user mod contains only one of those records in the form that it was before Bethesda's fix, the outcome could become interesting.

Personally, I would hesitate to even consider making a large mod at this point in time, unless it mostly consists of totally new records, that are guaranteed not to overlap with anything in update.esm.)