People always recommend epoxy over polyester, but I notice that Polyester Resin is used a lot in boat making and boat repairs so surely it can't be that weak?

There is actually a much more fundamental reason as to why Polyester is commonly used in boat building than cost and that is that most Epoxies are not suitable for use in prolonged contact with water as they can be hygroscopic and draw in water, especially non-marine variants. For the extreme end of the marine market (Volvo Ocean Race yachts, America's Cup, F1 Powerboats, etc.) Epoxy is used extensively but the hull will be coated with an external protective layer such as Durepox to prevent water ingress. This is a costly solution and hence reserved for the top end boats where lightness/strength is the determining design criteria and cost is much lower on the list of priorities. For the vast majority of marine applications, this is the other way round and longevity and cost-saving are above any other criteria and thus Polyester answers the requirements. Those hulls tend to be thicker and heavier than an epoxy counterpart but it is slightly difficult to compare because generally, an epoxy built boat hull is aimed at a totally different use to a polyester built hull.

My thought process was in relation to kayak use (so not left in water for prolonged amounts of time). I'm trying to figure out the benefit of using Epoxy for the construction when it's twice the price. 

I mean if you compare the inter-laminar shear strength between an epoxy laminate and a polyester laminate that have been submersed in water for a period of a year; the epoxy laminate will retain 90% of its strength whilst the polyester will only retain 65%.