Hell, I feel like there will be a bunch of plot holes surrounding this whole thing. It's useless to debate for now cause we have almost no information. I just have a feeling that he knows, but it's only a feeling. There are so many questions to ask tho.
First I entertained the idea that Shanks cried cause Roger told him that he was a CD. Then I asked myself how would Roger know that Shanks is CD? Did Roger find out during God Valley? Or did he think that Shanks' appearance reminds him of Garling? Did Roger pirates try to search for his parents? How and when did Roger pirates connect the dots? Did Garling try to take Shanks back? Is there a third party who, perhaps, could inform Roger pirates? Why was Shanks put in the chest in the first place?
Another possibility is that Shanks found out later. Did Garling even know that Shanks was with Roger pirates or nah? If he didn't he prolly saw Shanks' poster and went "hell, he looks exactly like me and Shamrock, I also happen to have a long lost son, guess it's him". Later Figarlands approached him and tried to get him to join CDs.
Edit: or they went "ew, he was touched by dirtycommoners and pirates, we should kill him so he doesn't disgrace our name".
Do Shanks and Shamrock have one mom or different moms and both of them just happen to look the same cause Garling has strong genes? Should we rule out clone theory? Also, if Shanks knows did he ever tell anybody about it or nah? Is he ashamed to be a CD?
And ofc it's possible that he doesn't know.