Let me begin by stating that I do not really know what I am doing... I do this as a hobby, although I do remember some things I learned 30 years ago studying aerospace at the university.
In short, what I do is use XFLR5, a program intended for analysis of model airplanes, that internally uses XFoil. It is possible to input viscosity and density of the analysis, so I use that of water instead of air, and that seems to work. I simply watched Youtube instructions and click around in that program, designing airfoil sections and wing configurations until I have something that I like, then I design it in cad, 3D print a mold or plug, build it from carbon fiber and try it on the water. I have some help for building and testing, my skills are limited. My designs optimize for stability and behavior in the waves, performance and speed are less important. I found there are many practical things that the software can't predict, the hardest part is understanding what to design for. Still, I think doing this leads to better results and better understanding than not doing any CFD calculations. I think my designs are better than the majority of commercial products.
To get back to your question, yes, XFLR uses the Vortex-Lattice method. It has several limitations:
http://www.xflr5.tech/docs/Part IV: Limitations.pdf. As I understand, main foil and stabilizer can interact, but the wake model is simplistic (flat) and their advise is to try to avoid interaction, the results are probably unreliable.
If there are better ways to analyze foil-wings or complete configurations (including mast and fuselage) on a budget, or you have additional tips, please let me know!