doing an "ac3d list" command via a telnet window gives the list of commands and one is:
boolean <subtract, union or intersect> "perform a boolean operation"
In a script, you'll need to select one object e.g. objectA, then another e.g. objectB and then submit the command "ac3d boolean subtract" which should perform objectA-objectB.
To find out more about how the internal commands are used, have a look in the tcl files (in the tcl subdirectory). If you look in the hierarchy tcl file, you'll see commands that work with object ids.
If you are a coder, it's relatively easy to add extra commands via a plugin. There are currently no commands to construct a object (e.g. create-object, add-vertex, add-surface etc.) but they could be added. They could be rather dangerous
e.g. you could accidentally add the same vertex twice or create a bad object which could cause AC3D to crash, but if used correctly, might be useful for your needs.