I take a somewhat different approach. West Point does not want to lose an appointee because of lack of information - this includes admissions, department heads, and others. If you have not received an appointment, there is no need to reach out to a department head.
If you have received an appointment and you have a question that materially affects your decision, you should not hesitate to find the answer, no matter who you have to contact. You will not lose your appointment because you emailed a Colonel. If it does not affect your decision on accepting the appointment, it can wait and will certainly be answered when you are a Cadet.
However, there is a caveat - it should be a substantial question that you have been unable to get an answer to after considerable effort. I can't really think of something that would fall into that category. Most information can be obtained through the website, Redbook, FFR, RC, etc. But if you are going to turn down an appointment because you don't have an answer to an important question, there is no downside in contacting anyone who might have the answer.
Colonels and Generals are people, just like CEO's and senior executives. Most are happy to help with a legitimate issue within their organization.