I went through this a couple months ago. Yes, all the 3DC templates are table-based. It is something they want to change in the future, but they are staying with it at the moment for maximum compatibility.
What I did is have my photoshop design converted to a CSS+HTML layout using psd2html.com. It was inexpensive and quick, and the results were perfect. I then used these files for the frame.html file in my 3DCart site, it's not hard at all to implement that aspect, just copy in some of the proprietary elements which are usually just variables.
You can see the results at my site,
http://beta.aebike.com
The front page is 100% CSS based.
HOWEVER, you will run into trouble on the sub-pages. I have managed to get a few subpages converted to CSS-only, but the prospect of converting all of them gives me a huge headache. There are just too many tables. And frankly I am not sure it's entirely possible, because the 3DCart templating system, for example the bit that will automatically replace variables with entries from your database, like products, seems to require that they be inside a <table>. You will find a ton of extraneous <tr> and <td> tags in your source code if you try to use their database variables without tables.
I pretty much just decided that I am ok with the tables on the subpages.