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The company cannot be charged with hit & run. Although some offences apply to corporations (e.g. violations of securities regulations, etc.), hit & run is not one of those offences. Just like a company cannot be charged with assault or murder.
That being said, if the person who was hit becomes aware of the culprit, since X was driving the company vehicle, the person who got hit could not only sue X but also the company arguing that the company is vicariously liable for X's actions and also that the owner of a motor vehicle is responsible for that vehicle (civilly, not criminally in this case).
In summary, your company car being involved in the hit & run could lead to a lawsuit against the company (albeit one which automobile insurance would likely cover) but I cannot see any way it would lead to criminal charges for hit & run against anyone other than the actual driver.