Now I'm not up to date on how colored coins work, but AFAIK they use OP_RETURN, which segwit will not change. Segwit will not change the output scripts except for maybe adding a new op code.
Most transactions use only OP_RETURN, but some of them use ugly hack which uses 1-of-3 multisig to store more than 80 bytes of data. I know, CC guys made ugly thing, it was not polite to make hacks.
![Sad](https://bitcointalk.org/Smileys/default/sad.gif)
It looks like CC should change the way they work completely. For example, there is not way to use multisig channels for them.
![Sad](https://bitcointalk.org/Smileys/default/sad.gif)
May be CC sidechain should be created.
![Sad](https://bitcointalk.org/Smileys/default/sad.gif)