I used the FP shared borders previously, though I came across a glitch where FP liked to delete them every now and again (im sure it was a glitch with the way it stores temporary files).
As far as I can remember of them, they should not affect ranking in any way. The additional code is placed inside a tag in the head which the frontpage extensions interpret. It should have something like "l r" if you have left and right side includes. I cant remember the exact syntax of the tag.
Nonetheless, the shared border is very similar to the "include page" function in frontpage. You may find these useful on your travels bsand, as it means you are unrestricted in regards to your usage of real estate (screen space) without the FP shared borders boxing in your main content.
I use the "include file" function for navigation. It saves you file space and the time it would take to update all the pages manually....just as the shared borders do.
If you look at the source code of your page on the web server, you should be able to see any extra code created by the borders...if there is any....but essentially WYSIWYG in regards to what you see on the screen....the SE spiders will see more or less the same.
FWIW I was using the shared borders with a site with PR6 in Google....so it was on the up when I was using them, I dont think they will harm your rankings at the very least.