Kinda cheesy I know, but it works!
Viewing post in A Simple Life with My Unobtrusive Girl comments
As far as I know, using cheats will just grant you the "ZAKO" title, aka the noob title. This only affects 2 things, 1st being how Imuoto and Aki address you, and 2nd being that it gives you a 20% damage reduction. As for story and progression, it doesn't touch these, Dev said so on their DLSite page which has all the cheats listed and tells you how to use them. If the ZAKO title alone scares you away from using the cheat codes, it can actually be disabled now in the most recent patch 1.08 rev4, just navigate to the settings menu while in game and it's at the bottom.
Long story short, using cheats should not affect anything in the current build or future updates as the only "negative" outcome to using them is receiving the ZAKO title which is really just a joke/easter egg and can be disabled anyway if you find it bothersome.