As I understood from both modders,
The model is the same, but the TGA files (green / red and cardinal) can be altered using a file. AFAIK, that will not drastically increase loading times. Lets give them time and I am sure they know what they are doing. DD allready stated that a solution was allready at hand in order to avoid the environmental folder to be a collection of far too many buoys.
As for loading times I'll tell you this:
My rig:
Athlon 3200
Ram: 500 megs
Geforce 6600 SLI 256 MB
I sometimes need to be patient when I load a Campaign, but that is a good thing, my dishes get washed that way

. Once my pc has loaded everything, it runs as smooth as a high-end mother. I would't worry about buoys too much if you have a few Highpoly DD's out there.
As for coastal navigation, you could have an almost perfect pinpoint accuracy when having a buoy system in SH3. The fact that the CTRL-Click method IMO is a little bit going around the roundabout twice when you can pass a buoy, go to you navigator and say 'plot the course for Kiel throughout the canal NOW !'
If you really need to pinpoint exactly where you are, then all you need is a decent map with 1 lighthouse position. 2 is nice but I imagine if you do the manual plotting of targets in SH3 you can use the same triangulation method for navigation. Look at the article on uboat.net that I posted earlier if you're interested in this. This may be a little hardcore to some, but it's good training for me as I want to start sailing next year.