Semantics schmemantics. The term "self-employed" is bandied about a lot, not least by HMRC in their literature, but it does not appear in statute. It's universally accepted meaning however is to refer to someone who is a sole trader or an individual in partnership, undertaking a trade, profession or vocation. If she operates exclusively through a company she would not be "self-employed" as universally understood, but would be employed by the company under her control.
As long as she is not caught by IR35 then there currently remain some incentives to operate through a company, if she can keep the admin costs down (especially accountancy). Leaving aside the potential NI savings, there are possible commercial benefits in attracting work if, for example, some customers will only deal with companies (to escape employment law and PAYE obligations), as is common in the IT industry.