Well yeah - of course if something is huge - and can be climbed on - it will be accounted by the server.
I don't think this will be a problem though. CS:Source has about 20 barrels lying around the place that are server side - and there's a few other things that are server side too - a tire and about 5 crates.
I don't know what doom3 were playing at with their netcode (2 barrels takes the same netcode as 28 players?) - but Half-Life seems to do it right.
In CS:Source there are lots of objects that aren't kept track of server side - simple things like milk cartons and glass bottles that doesn't interfier with the players movement/view.
Also bear in mind that there are quite a few 64 player CS:Source servers with no lag at all.