There was recently a similar conversation about Bootstrap + jQuery vs understanding core languages here: jQuery - Change the CSS of an Element Using jQuery
Unless you are told to use a specific technology, as a freelancer I would think you pretty much can use whatever you like as long as you fulfill the requirements. There are still plenty of Bootstrap/jQuery/PHP sites out there. The vast majority of sites are not made by 10x developers using all the latest and fancy tools. You can do a lot with simple tools as long as the requirements are simple.
However, relying on Bootstrap and jQuery will ultimately limit your options. I would make sure you learn the underlying technology (CSS/JS) so you can break out of the limitations the tools might impose, or more easily move to new tools.