C-language comment style has become an industry standard. There's nothing wrong with using # comments at all unless the particular coding standard for your project or workplace prohibits it. Standards are the key to yielding readable code.
In many cases, // and/or /* */ are considered standard comment syntax for programming languages. The only exception that commonly is encountered is VB, which uses '. In contrast, # is often considered the standard comment syntax for shell scripting.
PHP was designed to perform both tasks originally. PHP can and does function reasonably well as a shell scripting language and can be invoked from the command line. It has functions to handle reading from stdin and writing to stdout. This is probably the origin of the # syntax for comments. # is probably discouraged because PHP is thought of as a programming language nowadays, rather than a tool for shell scripting. Specifically, the style guides that the question references are for web apps, rather than some shell tool.