When I apply dt:theme="bootstrap2|3" to a table, I get a strangely formatted pager as well as multiple sort icons over the same location. I'm using a fairly basic setup in an example application with no bundle overrides. I haven't defined any properties files, either. I'm only adding the theme on the table; no bundle-includes at the top.
Perhaps another option is to have the themes not depend on "datatables", and they would redefine the assets that are required. If a theme is specified, "datatables" is no longer added as a dependency; only the theme, which has all it's assets defined.
Another way to think about it is that there are multiple themes, and "datatables" is just one of them (and the default). If a different theme is specified, then that one is used, and the default is not included. Only one theme can be in play at once. Does that make sense?
I'd like to suggest that you add this to the list of known issues in the docs.
I spent about 2 hours tracking this down, and was about to submit a bug report when I found this thread.
The fix is simple, and I understand your position of letting the developer decide which library to disable, and I don't disagree. I just wish this issue was documented as it would saved me a bit of time.
I see this as a known issue with a known solution.