How to efficiently trim 3mm polycarbonate with portable tool(s)?
If you have to use an unpowered hand tool, then a file or possibly a hacksaw will work.  Anything with coarser teeth than that (like the saw you linked to) will be very difficult to use on such a hard material and cracking is likely.

If you can use power, a belt sander will work.  An angle grinder iwth a cut-off wheel or Dremel tool will also work, but they can be a hassle to use if you have a long cut because they cut slowly and stink because they melt the material as they go (use in a well ventilated area).