How can bitinfocharts.com know the changes in BTC deposited to Binance?
Based on the address the binance gave you, after they sweep the funds into their hotwallet, you can run common-input heuristic on this deposit address (assuming it was swept in with other inputs). The more addresses and sweeps, the better the accuracy and amount of addresses in the final (result) set. 
https://en.bitcoin.it/wiki/Privacy#Common-input-ownership_heuristic
Based on the binance hotwallet you can also assume that all addresses that inputs into this hotwallet are deposit addresses.


Having set of all (assumed) addresses of binance you can run basic script to see balances in/out.