X9 is just a file format. The FRB adopted it for Check 21 purposes. JH can accept both formats and convert them to a format that can be used in their ImageCenter, SuperImage, and 4|Sight systems. I don't think it is avaialbe to all JH clients - just those on the SilverLake System®, CIF 20/20®, and Core Director platforms.
I've not audited use of these systems, but my gut is to treat this as outsourced data processing. I'd look for data integrity, consistency, and completeness of the X9 data files sent and received. If customers are uploading their own data files directly, I'd also look for controls to ensure the checks actually exist, although I suspect you'd see an uptick in returns if they didn't.
The link below is to the last FRB standards update on Image Cash Letters that I recall seeing. It gives a little info. on the X9 format. Image Cash Letter Customer Documentation