The "detector" part of the name is a bit disingenuous. Sites like this are not actually traversing through your plugins and themes directories and cataloging everything that's in there.
They're scanning through the source of your webpage for known plugin signatures. Something that any human can do by right-clicking on the page and selecting "View Source."
Like if there's something like "<!-- page cached by WP Super Cache! -->" ...it would be safe to assume you used WP Super Cache. (I don't know if WP Theme Detector actually does this, but they could.)
Or if you have a stylesheet link to /wp-content/themes/some-detected-theme/style.css with the default theme style header information (which includes theme author, theme URI, description, etc.), it could see that, just like any person could see manually.
The only way this would be possible to actually "detect" everything is if you allowed the public to see your directory indexes. WordPress usually puts a blank index.php file in directories to prevent this from happening.
Anyway, to answer your question:
1) Make sure that you can't see anything at example.com/wp-content/plugins/ ...if a directory index is displayed, then anyone can see that. This probably won't happen unless your server is configured weirdly.
2) What other plugins do you want to conceal? If the presence of a plugin you want concealed is apparent in the public source code, you could rename the plugin and obfuscate other public "clues"...but that would be a lot of work and would be a huge pain when updating. Otherwise, there's no way to know.