CLS55 will cost more no doubt, allot more things to go wrong, the CLK55 will be cheaper to run, it's nice and simple.
Cls55 was over 80k new the 209 clk55 was around 50k..
Both will have similar vehicle tax (unless disparate ages either side of the change of bands in 2006), both large V8s so similar on servicing and fuel costs, insurance likely to be similar and depreciation the same (arguably a CLS is better looking so I would argue the depreciation would be less overall).
Only the difference in mechanicals with air suspension and SBC, if buying from that era, and they don't go wrong that often.
I can't imagine the parts are much different in price either.
You can of course be unlucky with any car but I doubt there is a lot in it all said and done.