The question is regarding "Security through obscurity"1. Does hiding your design/implementation (e.g. what server you are running) lead to less instances of exploitation? This is a long debated subject with reasonable arguments on both sides of the fence.
All security practices are a tradeoff between cost (e.g. effort, maintainability, money) and benefit (reduced instances of exploitation, reduced impact of those inevitable instances). In this case the cost is the effort it takes to change the string and the benefit is some degree of obscurity. However, (as you noted) in a targeted attack (and by that I mean someone is determined to get into your systems) there are other methods of canceling out that benefit (e.g. looking at default error pages, default files, obscure stuff like cookie handling, and pwning something else). In a non-targeted attack (and by that I mean some skiddie looking for low hanging fruit or a dumb automated piece of software scanning the internet, same thing) you avoid harassment.
HOWEVER, the actions needed to secure against a targeted attack (regular updates, access controls, sane configuration, good data hygiene) would protect against aforementioned non-targeted attacks. These are by far the best bang for the buck and what you should be doing.
So, if you are out of other things to do, then go ahead and hide your server tokens. It'll stop people from noticing low hanging fruit if you are super late applying patches or something else fails. However, note that in that case you may already be dead in the water. So if there is anything left, your time is better spent attending to that or asking good questions like this one.
Personally I prefer adding humorous server tokens to make attackers laugh or incorrect server tokens to confuse them. minorcrash.com (when up) currently has DOM injection that renders a picture of a cat being hit by a snowball.
