There is no such thing as a multi city ticket. The Emirates website (and many OTAs) have a multi city search option which is useful when your return departs or arrives at a different airport than your outbound, you have more than 2 segments on your itinerary, want to add a stopover or force a specific connection. The resulting ticket is still a regular ticket. It just give you a hit more control over the flight combinations and sometimes fares. Because the STL flight is operated by AS (and btw I'd also look for B6 connections) there might not be a fare available from DXB-STL so the website just says "sorry, nada" but if you feed it each leg separately it can find the EK fare DXB-SEA and price the separate AS fare to STL.
The above is mostly my conjecture on how pricing works. But to answer your question, yes you'd be protected. Virtually every flight I book is a "multi-city" flight. Also EK isn't AA, it's rare to be more than 30 mins late, let alone an hour or two.