1) Yes you can delete the visible .DS store files
THere are various ways of automating this process , too, by the way. See
http://www.redroomdevelopment.com/products/dsstorecleaner/ or
http://www.macromedia.com/cfusion/knowledgebase/index.cfm?id=tn_16831 for a couple of options. Cocktail is also able to deal with this issue, from memory.
2) Whether its wise to simply copy your old home library or not depends to some extent on why you chose to reformat and re-install. My general advicen a situation where you have reformatted to solve a problem, is DON'T. Instead keep a copy of it for a while , so that any necessary items can be replaced individually.
Simply copying it back holus bolus may well reintroduce whatever problems you had to start with.
Cheers
Rod