Crypto system design : How to design Encryption for Zero width characters
First of all, the use of zero-width characters is what we call obfuscation and indeed stenography. The encryption part that is described seems separate from it.

Generally we don't encrypt each element separate, we encrypt the plaintext and then try to hide the plaintext. Encryption generally needs something to make the key / IV unique otherwise you would get the same ciphertext for identical messages. In your situation it is only safe to use a fixed IV if a unique salt is used for each key that you derive from the password using a password based key derivation function or PBKDF. Of course, instead of having to store an IV you'd now have to store a salt.

CTR mode only requires a nonce rather than an unpredicatable IV. The nonce is a unique value of any size. Because of that the overhead of using the IV is much smaller. Alternatively, if you're stuck to CBC + CTS, you can use a nonce as IV for CBC by encrypting that initial IV with AES to derive the actual IV. IN both cases you might need to right pad the (initial) nonce with zero bytes before you can use it.

I don't see anything about a PBKDF in your description so your design probably still needs a lot of work. However, you are seeing the problems and you ask the right questions, and at this stage that might be more important.