A number of my friends work in the policy-and-politics sphere - I can assure you they definitely do tally those, and it does make a huge difference, even if your Congressman is one of the sponsors of the bill.
Aside from the official counts that they have to keep whenever constituents call them, the main thing to remember is that these offices are small - even the main offices for senators like Schumer or Gillibrand (who represent big states) in DC are only staffed by a few people at a time. If they're flooded with calls from any particular group, what do you think they're going to be talking about over lunch, or at the (figurative) water-cooler, etc.?
A friend of mine worked for Senator Clinton around 2007, and she loves to tell the story of how they got flooded with fake "Valentines" from the Association for Heart Disease[0] the week of February 14th, in support of some bill. It was a pretty uncontroversial bill and passed with wide support, but just fielding those letters and calls took up so much of their time that week that she still remembers it, years later.
In short, please do call them - they'll remember it the next time they consider sticking their neck out for something that they believe is the right thing to do but may be politically risky.
[0] I don't know the name - you get the idea