Write a brief (1 to 2 page) plan for the CEO about how to 'better manage' licenses on company computers. The plan should focus on incremental improvement (what to install on new computers, what to install when asked on existing computers).
Have the plan oriented to save money and reduce obligations of share ware. Give a few options, but don't preach about software philosophy.
Advise the CEO, NOT IN WRITING, of some of your concerns for legacy computers, and show him that you're committed to continuous improvement in this area. Remind him that the BSA wields a heavy hammer, and to be mindful of angry ex-employees who might take advantage.
CEO's like plans with no immediate funding requirement, low stress on the organization, and continuous improvement. Write your plan assuming the BSA will eventually read it - that is, don't incriminate yourself or the company.
"Little else matters than to write good code." -- Karl Lehenbauer