He loved working there.

Every time we saw Bob working at Radioshack he seemed genuinely happy. Also, as stated in the question, he was smarter than most of the employees there thus he could safely call himself "Bob the brain" without being singled out. Here's a nice little summary of why he loved his job.

He loved working at Radio Shack, because at Radio Shack the other employees knew some things about electronics, but not all of the things like him, and so he could literally call himself “Bob the Brain” and no one would call him out.

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So, he was just happy were he was. In an interview Sean Astin (Bob's actor) said that he thought working at RadioShack gave his character free time to experiment.

“I haven’t talked about it with anybody else,” Astin said, “and I’m absolutely convinced that people will find this interesting.” Rather than pretending to be on the phone or jotting down a note, Astin decided Bob would be fiddling with some very appropriate Radio Shack merchandise. “Those needle-nose pliers and that wire,” Astin recalled fondly. “As far as I was concerned, that was the same thing as the Holy Grail.”

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Thus, he got to have fun and have some play time at his job, sounds pretty great to me!

If you didn't live through it, you may not be familiar with what RadioShack once was. It used to be that when you went to RadioShack, you could buy vacuum tubes for your TV (look it up), resistors, capacitors, transistors, etc. Back before we called makers makers, they were just nerds who bought stuff at RadioShack.

In the 70s, hacker culture was starting to take shape. Many people who were into electronics and home-built kits for radios and TVs also started getting into computers and phone phreaking. You would buy parts for your projects at RadioShack.

In 1977 RadioShack introduced the TRS-80 personal computer. It was a competitor to the Apple I and sold more units that even the Apple][ for a few years. By the 80s, you could get computer parts and software at RadioShack as well as hardware to build your projects. From the Wikipedia article on RadioShack:

Radio Shack's computer stores offered lessons to pre-teens as "Radio Shack Computer Camp" in the early 1980s.[47]

By September 1982, the company had more than 4,300 stores, and more than 2,000 independent franchises in towns not large enough for a company-owned store. The latter also sold third-party hardware and software for Tandy computers.

Likely a town the size of Hawkins, Indiana had an independent franchise. It would have been exactly the type of place a smart, small-town, midwestern nerd like Bob would want to work.