Possible? Sure. Difficult? Depends.
To avoid a crosswind the deck angle offset would need to be known. Maintaining an internal lookup seems troublesome; instead, I could read a new entry from the configuration files, but that would require users to define the deck angle for each boat. I suppose if the entry is missing I could assume no angled deck and put the boat straight into the wind, but that seems like bad user experience if users fail to make the modifications when there is an angled deck.
Also, since AI Carriers .NET is almost identical to AICarriers2r2, the main menus aren't very extensible. It probably wouldn't be too troublesome in this situation since there's room for one more option (since SimConnect text menus only have space for 10 options and only 9 are currently used), but additional changes beyond that may present a challenge.
Additionally, AICarriers2r2 (and thus, AI Carriers .NET) uses throttle to set the boat movement. To be able to have the secondary menu to select wind over deck would likely require implementing a PID controller (or similar), which may need to be configured per boat (as the acceleration/deceleration constants may differ). It might be possible to set the AI DESIRED SPEED variable and let the AI system control the boat, but from what I recall, using that resulted in small variations in speed, and there were some instances where the boat would yield to the user (i.e. stop each time the user taxied forward of the center of the model).
Like AICarriers2r2, AI Carriers .NET remains open source software. However, while AICarriers2r2 is public domain, AI Carriers .NET is available under The MIT License. Anyone is free to modify and submit pull requests with improvements should they desire.