When the companies are supposed to store most of their funds in cold wallets, how is it possible that they loose so much funds. Alternatively, if 107 btc's only accounts for lets say 3-5% which might be kept in the hot wallet, then it shouldn't matter as the company should be able to pay back their customers if not instantly, then within sometime by their operating incomes.

The fact however remains that if a Webserver has access to the wallets, their is always a possibility of hacking. There is not much any of us can do as the hacks keep evolving and if you dont know about a vulnerability, then there is not much you can do to prevent it. Its not like the Crypto companies are as big as google that they can be on top of everything. Thus, the only option is to sever the link between the webserver and the wallet server and still make them talk somehow. Its very difficult to do but possible.