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Google has followed all of those links and has indexed the interior pages.
It hasn't been a problem for me. Maybe others will post here as to their situations.
Templates are Ok for smaller sites, but I have a few sites with 2000+ pages each - you really get the benefit of changing just one file then!
You can also prepare different style sheets for different browsers etc
DWMX will automatically update the style sheet if you move layers around.
Its also worth checking out the free extension "Layer2Style", which is invaluable for moving all the positioning info into the <head> ready for plonking into the external css file.