The reason why target is deprecated is because frames are deprecated and frames are the only place where you need to be able to target a link. The rest of the time you should leave it up to your visitors as to what they want to open where.
To use frames you need to use the frameset doctype which also allows target. To use iframes you need to use the transitional doctype which also allows target. The only doctype which doesn't allow target is the strict doctype which also expects you to not be using frames and to have replaced all your iframes with objects.
So there is no conflict provided you use the appropriate doctype for what you are trying to do.