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I also use hidden counters on some of my sites that have the same color as the background. Clients like ability to see the page counts but not advertise it to the world. I only display numbers but could search engines penelize me for a number?
On the counter - if you are using font tags and matching the font color to the bg color, you could be tripping some alarms. If you give that counter content a class name and define the class in an external style sheet, you should do fine.
Even if you trigger a hand check with the external style sheet, it's pretty harmless and I doubt you would be penalized.