You know TB, you got me thinking that I know nothing about Sai and their usage, so after a half hour google and read up, I feel I can say this.
Sai seem to need 4 fingers and a thumb for correct handling, so Raph is immediately disadvantaged. However, not being one to let The Man get to my fave TMNT, I came up with this.
So it would seem that yes, he can hold them accurately. To a certain extent anyway...