People say this, but I've been outright told, twice, if I plan on ranking the program my number one come January to let them know as that is taken into consideration.
I'd imagine it still doesn't make a difference--a program really doesn't have any incentive to bump you up their list just because they're your first choice. But, they do have an incentive to make you think that ranking them first that it would increase your odds of matching there, as it might lead you to rank that program higher than you otherwise would have.
ie., I really want to rank program A first, then B second, but I know both are reaches and I may not match at either, but if I thought ranking B first would actually help increase the odds of matching to one of those "dream programs" then maybe I rank it first so that I can ethically tell program B they're my first choice and get the "#1 bump" they hinted at.
My guess is the programs that say things like that want to get an idea ahead of time whether they're going to fill their positions and where people who rank them #1 fall on their rank list--in theory if they have 4 positions and 4 people say "you're my #1" and actually rank them #1, then they now now they will do at least as good as the lowest of those 4 people. (Granted, programs would be smart enough to realize some of those applicants may not be truthful)
If you absolutely know you're going to rank a program #1, it probably doesn't hurt to tell a program. But I think what really matters to a program is that you genuinely want to go there--they likely won't change your position on the list because you rank them 1 instead of 2, but they most definitely would if they got the opinion you had no real interest in coming to their program (if they're your back-up, etc., then you might be miserable and bring down everyone in the program, or you might leave if a better opportunity comes by, etc.).
The other thing to consider is sometimes you will end up juggling around where to rank your favorite programs--it was pretty clear when I finished interviewing in January what my top three programs were, but I had a hard time ranking those three relative to each other. If I tell a program they're my #1 in mid-January then now I'm either "locked-in" to ranking them first or if I change my mind I risk alienating myself from that program and others (PM&R is a small world--people talk) if that program ranked me high enough to match but I end up somewhere else.