Are industrial bachelor/master theses worth it? We had a job fair at our university recently, and there were renowned IT companies like Cisco, for example, who offered us topics for our bachelor/masters theses (I'm double major in physics and math, they were interested in math students mostly). 

The question I have is, are "industrial" theses made under big IT companies worth it in fields of applied math/machine learning, in case I would like to continue to do my Ph.D. in future? Or is it better to do some "academical" thesis with this aim?

Thanks!
This is a common and healthy practice around the world. Companies are usually facing difficult problems that can potentially have many different solutions and are looking for the most innovative and efficient ones. Offering these projects to masters and PhD students saves money for the company and helps make the student more experienced in solving real-world problems. In addition, if you do a good work in your masters, it's not unlikely that the company may offer you a scholarship to do your PhD in the same field, which is extremely important. Not to mention that you can establish contacts with people from the industry.

There is really very little difference between what you call "industrial" theses and "academical" theses. In both cases, you have to do literature review, problem motivation, implementation, and evaluation. All of that has to be in the thesis. Also, both pave the way to do your PhD in the same or similar fields.