By keeping count like this there is a chance that, if you keep it as a habit, it could develop into a problem. Whilst muting and picking can be used as a musical idea, and indeed I use it occasionally to fill out rhythms on my bass, unwanted sounds can be picked up, and if amplified are not particularly desirable. Even muted I personally won't go near the strings as with various effects pedals that can be very sensitive even the faintest touch can produce unwanted sounds.
When I was playing Cello and would have huge sections of breaks I would lightly tap my feet whilst counting, which worked well. Whilst practising try using a metronome and make a point of not touching the strings whilst you are in a rest to try and improve your awareness of the rhythm. You can also practise different time signatures and styles over time, and again a metronome, or a drum beat behind will help. In a band situation you get used to the pieces themselves, and I'll have reference points from the other musicians (assuming they play it right...).