Got it, thank you! There are a few issues to deal with.
First, the input data seem to have an incorrectly defined coordinate system. The system is defined as,
Name: EPSG:32619 - WGS 84 / UTM zone 19N
Units: meters
But the coordinates, such as the extent of the AOI, are,
109.6206202631684050,18.3593145628195771 : 111.6610080756678940,20.2212427998816224
With units of meters, this makes the AOI only about 2 meters x 2 meters wide. Instead, these coordinates appear to be decimal degrees (longitude, latitude). So, if I redefine (not reproject) the coordinate system to a geographic system, such as EPSG 4326, WGS84, then the data appears to make sense.
You can verify these things by looking at your data in GIS and adding a reference map, such as data from Natural Earth » 1:10m Cultural Vectors - Free vector and raster map data at 1:10m, 1:50m, and 1:110m scales
Second, for this model, it is not a good idea to clip your input data to the boundary of the AOI. Please see the Area of Interest section of the User’s Guide for more details: Coastal Vulnerability Model — InVEST® documentation
In particular, it is almost always best to use this model’s sample data with global coverage for the WW3 layer and the continental shelf layer. The landmass and bathymetry layers also must extend well beyond the AOI in order to have accurate wind & wave results, based on the ray-casting function.