Cydia doesn't respect the Settings->Sounds Keyboard Clicks toggle. As seen here or here. Other jailbreak apps like iFile have the same problem like here. In case other people on the web are looking for a solution I thought I'd post my success.
The reason is that these apps are looking at the var/root/library/preferences which does not contain a com.apple.preferences.sounds.plist. so it uses the default value of On for the keyboard clicks. Setting a symlink for the com.apple.preferences.sounds.plist in the root preferences directory to point to the mobile preferences directory fixes the issue.
Here is the file you are linking.
I did all this on my iPhone using iFile but you could just as easy do it using SSH or whatever.
Navigate to mobile preferences directory.
Copy/Link the com.apple.preferences.sounds.plist
Paste the link in the rooth preferences directory. Here is the root preferences directory showing the symlink in blue.
The reason is that these apps are looking at the var/root/library/preferences which does not contain a com.apple.preferences.sounds.plist. so it uses the default value of On for the keyboard clicks. Setting a symlink for the com.apple.preferences.sounds.plist in the root preferences directory to point to the mobile preferences directory fixes the issue.
Here is the file you are linking.

I did all this on my iPhone using iFile but you could just as easy do it using SSH or whatever.
Navigate to mobile preferences directory.

Copy/Link the com.apple.preferences.sounds.plist

Paste the link in the rooth preferences directory. Here is the root preferences directory showing the symlink in blue.
