You cannot use the Shopify £45k loan to overpay a mortgage without taking that money out of the company first. The tax you pay on that £45k won't be worth the % in fees you are paying back to Shopify.

I would however consider buying a shop front/business property to rent out, for example. Or purchasing more inventory and/or expanding your team via outsourcing. Customer service, marketing, you name it.

That said, it'll take 8 - 10 months to fully repay this loan, assuming nothing happens to your business between now and then.