Problem:

There is an issue (either in the .ase format itself, Q3Map2 or Quake 3) with a single .ase model file containing more than 1024(?) polygons with regards to smoothing groups. ASE models with greater than 1024 polygons will result in odd smoothing group issues that can't be solved by conventional means. The only solution I've been able to find is to split the model into separate smaller models and combine them in the editor. Rather annoying, but that's what you get with working with older technology where 1024 seems like a great big number. Not so, these days. Still experimenting to find the exact cause and reproducibility of the issue.

Update

It is not caused by:

Instead, it looks like it is purely based on 1024 polygons per model. Might be resolved with a phong shader (haven't tested). No current solutions.