As they share the same Reference Manual they should be fully compatible for everything that is present on both microcontrollers. But do compare the Data Sheets as well.
Your programmer might grumble if you haven't recompiled the code for the other part, and their device-IDs differ.
Problems might be encountered if you do not fully follow the instructions in the Reference Manual e.g. where bits of certain registers are labelled "Reserved, must be kept at reset value" and you write anything else there for convenience or through carelessness. But then those problems might also be seen if you try to use the same code on a different revision of the same chip.
My suspicion is that these devices are based on the same silicon die, but ST disable the crypto bits to allow them to sell it where they're not allowed to export such cryptography technology.
It's also possible that the crypto unit failed its production-tests on certain chips, and ST chose to sell them as parts without crypto rather than scrapping them entirely. (Many failures in chip production are due to a speck of dust landing at an unfortunate spot and knocking out a single transistor or connection; all other parts continue to work perfectly).
