I've always believed that vertices that lie off/in between the 1-unit grid snap to nearest unit. The result is that you get cracks in walls, caused by carving a cillinder into a wall for example or you get deformed brushes.
That's why HLFix was invented. HLFix basically replaces the EXPORT TO .MAP feature in Hammer as it generates a .map file on its own. The major difference is that, as CStriker pointed out, HLFix exports a .map as floating points instead of integers which no longer causes vertices to snap to the nearest point. The result is that rotated and/or twisted objects no longer look deformed ingame.
However, there appears to be some compatibility issues with HLFix and the latest SHLT. Known issues are outside world errors and dissapearing faces.
So right you want to
- Use HLFix to generate the .map file which has floating points instead of integers but in return you're forced to deal with possible compiling errors and disappearing faces
- Stick to SHLT and not use HLFix to get around the compatibility issues between HLFix and the other tools but you're back using integers again causing cracks and deformed brushes due to off-grid vertices.