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.
It looks like CC should change the way they work completely. For example, there is not way to use multisig channels for them.
May be CC sidechain should be created.
