Disabling the stock message app shouldn't cause problems - message apps are just a front-end anyway, and separate from the underlying SMS service. The stock message app on my phone is Google Messages, and I keep that disabled with no ill effect (as I have the stock apps on my previous phones). Since Contacts Storage is a separate app from the phonebook I would think that the same would be true there.
However, it may well be that Samsung have decided not to give you the option. Ideally they should only withhold the option of disabling an app if it is vital to the system, but different manufacturers apply different policies here. I've known Samsung withold disabling quite arbitrarily for their own apps and even for 3rd party junk that they decided to include in the ROM (and as I don't buy carrier-branded devices this wasn't a carrier's choice, though they can also indulge in that).
However, if you use a third party launcher (I don't know about the built-in one) you can hide them from the app drawer so you never see these apps and just use your preferred one. Force close them if you like. If you never use them the system's optimisation should stop pre-loading them eventually, and hence the fact that they are still installed shouldn't cause you any problems. I use the Google Contacts app on my tablet and the fact that the Samsung one is not disabled doesn't interfere with me in any way.