Washed my bike with water and muc-off only, now my brakes are weak I took part in my first bike event at the weekend, a very muddy "gravel" ride which by the end had my bike covered in mud! Rather than put it straight in the car, I took it to the muc-off tent and cleaned it with a little of their spray (mainly on the chain/cassette/crank), water, and a soft brush. When I got home I applied wd-40 to the aforementioned parts only.

Riding it today I noticed that my disc drakes were much weaker than they were before. Given that I haven't used any soap, or applied oil to the rotors, am I right to think that this should improve with use and that I haven't ruined my pads? They're only a couple of weeks old!

Thanks :)
No, they probably will NOT get better without help.

The cleaner that you used is probably the problem. Maybe WD-40 overspray too; that stuff gets everywhere and it only takes a bit to ruin your brake pads. BTW WD-40 is usually NOT the best choice for ANYWHERE on a bike.

Disc brakes are great in a lot of ways but they have a couple vulnerabilities. One of these is that the pads can be contaminated and then the brakes don't stop well. Although you can soak disc brakes in mud repeatedly and they'll be fine, a drop of a solvent, cleaner, or lubricant can ruin the pads permanently.

No matter if they're "mechanical" cable-actuated, hydraulic with mineral oil or DOT; bottom line, the brake pad material is super sensitive to fouling. I got brake fluid on my (metallic material) pads years ago and brought them back to life by removing them and soaking in various solvents including alcohol and acetone and scrubbing with a toothbrush. Another time I got an unknown contaminant on organic pads, tried the same technique and... all I got was a bunch of contaminated solvents and another trashed toothbrush. I even tried sanding the pads and they still didn't work.

So, you can try the remove-soak-scrub-sand technique, or go buy yourself some new brake pads. 

Just make sure the braking surface on the rotor is CLEAN before you put in the new pads.