The only thing "added" by that app is the international keyboard icon (which would be added for ANY international keyboard you added...and is an icon addition written IN apples own software for the messaging app)...the emoji app just adds another keyboard to the list, it doesn't change any dimensions in the default keyboard that you use, nor could it effect the keyboard inputs themselves (IE: causing false letter strikes, etc).
Should you be worried? I mean thats on you, i don't worry about it because its not that big of a deal to me, you might be one to blow your own head off over things like that, which would mean the "worry" level would be different between us, lol.
If you're still stressed out of your mind about it after reading this...go to the Apple store, where they'll tell you that iEmoji is a 3rd party app, and they don't recommend using them for this or that or whatever...and then you won't be able to replicate the issue for them, so there won't be an issue for them to fix, and they'll give you a big friendly thanks as you walk out feeling the exact same as you did when you walked in...
That or tie a model rocket to your iPhone and send it to the moon...that'll alleviate the issue.