This option is hardcoded now... So It is obsolete you can't change it...
eDonkey clients and servers use protocol numbers to check their compatibility. Server administrators can setup their servers to reject clients whose reported protocol version is not within some range, to get rid of obsolete and incompatible clients.
You know you're being rejected if you see
From server: ascii: ~[[(5)]] dec: ~[[(5)]]
in core output.
Setting protocol_version to the right value can be useful to stay compatible with some servers, even if it doesn't otherwise modify the protocol MLdonkey \"speaks\".
update: This post I found on Overnet forum provides some insight on what the protocol values mean: http://forums.overnet.com/phpBBovr/viewtopic.php?t=47074