Generally yes. A franchise fee that has been paid and cannot be recovered is capital irrevocably committed and at risk. Equipment and inventory actually purchased count as well; refundable deposits and unspent working capital do not.
At risk means gone if the visa is refused
The E-2 rules require the investor's funds to be irrevocably committed to the enterprise and subject to loss if it fails. A nonrefundable initial franchise fee meets that test the moment it is paid, and consular practice treats it as part of the investment together with the cost of the van, tools, software, signage and opening inventory that have been bought outright. What does not count is anything the buyer could still get back: a deposit that the franchisor returns if the visa is refused, money held in the buyer's own account for future expenses, or a loan the buyer is not personally liable for.
Substantiality is then assessed against the total cost of establishing this particular franchise, so paying the full fee and equipment cost is usually enough. The fee alone, with everything else still unspent, may look like a plan rather than an investment. The buyer must also be a Canadian citizen and must own and direct the business, which sole ownership satisfies.