A young colleague of mine forwarded an email to me that he received from my boss wishing him a happy Easter and telling him how much he valued his contribution and that his hard work had not gone unnoticed!
I was just reading over this again and one thought occurs ... this is a young colleague and your boss states that "his hard work had not gone unnoticed" is there either currently a promotion/vacancy or is there about to be one that they wish to encourage this young man to apply for. With legislation the organisation has to be careful about letting employees know they're considered a suitable candidate and the informal message you have seen would be an acceptable way of flagging it up.
Like the others have said, what you cannot see is the context in which this statement was made ... there are many scenarios it could fit.
You also have received good advice that if after sometime you still feel the same way about being undervalued you need to seek a discussion ... but only if you truly do feel that way.
However, I too subscribe to the theory that, if your boss never wishes you well for holidays or sincerely thanks you, you can lead by finding suitable opportunities to offer positive reinforcement to your boss; so "I have heard very positive comments about the budget briefing you delivered on Monday ..." even as far as " ... everyone is talking about that Powerpoint slide we worked on to illustrate X, Y, Z" There is nothing wrong with identifying your contribution with his success ... but don't fall into the trap of "everyone thinks that slide I redid for you made the whole briefing"
Good luck
Cathy