I have not tried this specifically, but you should be able to create a manual property (either style- or object-based) for your Door/Window Assemblies to hold the door thickness information, which you would need to enter manually.
In a property set applying to both Doors and Door/Window Assemblies, add an automatic property referencing the Object Type automatic property source. Then, set up a formula property that tests the value of the ObjectType property - if it is "Door", pass through the thickness automatic property for Doors (which you presumably already have). Otherwise, pass through the manual property value for Door/Window Assemblies.
You will want to replace the door thickness column in your Schedule Table Style with the new formula property.
Sorry, no time right now to offer a detailed, step-by-step or post a sample file where this works. Post back if you need more details, preferrably with a sample file showing your progress. You can also find general information on overriding values with formula properties as well as other information that may be helpful to the task at hand in the following articles in my blog:
http://architects-desktop.blogspot.com/2007/04/aca-2008adt-2007-setting-different.html
http://architects-desktop.blogspot.com/2007/03/another-formula-property-override.html
Here is one that does something similar for Windows & DWAs for frame depth (follow the link for a thread that has a 2005 sample file):
http://architects-desktop.blogspot.com/2006/01/doorwindow-assembly-frame-depth-in.html
http://architects-desktop.blogspot.com/2005/07/unformatted-properties-and-numeric.html
http://architects-desktop.blogspot.com/2005/07/structureflow-in-formula-properties.html
http://architects-desktop.blogspot.com/2005/01/unformatted-properties-for-formulas.html
http://architects-desktop.blogspot.com/2004/12/overriding-property-value-using.html
If you need to use the revised schedule table in a file that has your old property sets, you may also want to read this article:
http://architects-desktop.blogspot.com/2007/04/revising-schedule-table-style.html
--
David Koch
Using ADT 2004 at work; access to 2005-2009 at home