It's a pretty sure bet that both the 45mm and 90mm will be updated soon.... although exactly when is anyone's guess. And, you can bet that the new versions will be substantially more expensive than the current versions.
Based upon the design of the two new lenses, the main thing to expect with the new versions is that the lens will have dual rotating assemblies.
The current versions of these lenses have a single rotation plane, allowing the lens to be rotated and oriented as needed, such as to switch from rise/fall shift to right/left shift. However, from the factory the shift and tilt functions are 90 degrees out of phase with each other. It's possible to send the lens in to Canon service and have them aligned, if you wish. But it's a relatively permanent change and not easily switched back.
The Mark II versions of the lenses add another rotational plane feature, so the user can either align or deliberately misalign shift and tilt, as needed and right there on location, with a simple press of a button and turn of the lens.
If using the lenses for small items and table top work, you might choose based upon the camera you'll be using. On a full frame camera, you might select the 90mm. On a crop, the 45mm works great. One of the key considerations with this type of work is a focal length that allows you to reach out and rearrange small items while keeping your eye to the viewfinder. If you tend to work with a tethered laptop and have room for more working distance, this might not be as important a consideration.
