Yeah there are some differences between the two but not very big ones and it depends on if you really want the new features on the 2000.
I personally have a 99 CLK430 and LOVE it. Ive had it for two years now and what Ive noticed that the 2000's have are what you mentioned before, mirror blinkers, but they also have a different shifter (Instead of having one spot for first gear and second and so forth you just slap the shifter to the left and push it up or down to shift "Manually"). But what they don't, apparently, have is the fancy Chrome accents around the windows which I personally didn't notice that the 99's were the only year to come with this standard but now that I do... Its really cool.
So like I said it really depends on if having fancy mirror blinkers, or the fancy chrome trim around the windows matters to you. Personally having a W208 is a joy in itself and I would go for which ever one has lower millage so you can enjoy it that much longer.
P.S. If Im wrong on any of these statements, which I might be, please feel free to correct me

. Im sure yall will. haha