I dont have a garden railway, but I've listed a few commonsense points.
Dont ever be tempted to leave any of your locomotives & rolling stock outside overnight or when nobody's at home, keep loco's, rolling stock & the transformer controller or DCC control box etc safely stored indoors.
240v extention leads must also be kept indoors OR a permanant 240v power supply cable & its 3 pin sockets must be adequetly installed with exterior grade armoured cable in trunking & buried as to protect from the weather & possible accidents chopping cable with the garden spade etc.
To deter cats from damaging scenery , I've heard say that if you leave a few pieces of orange peel lying around , cats do not like the scent of this & will avoid.
Possibly install some cctv camera's with infered & motion detection / PIR activating a recording device of some format VHS, DVDR , HDD etc ,
How large is the layout ? I assume the layout is on trestle mounted baseboards , what are the baseboard frames & baseboard top / trackbed made out of ?
You'll need to weather proof all wood & plywood. I use Saddolin stain to protect the timber of my shed & back gate , but if not Sadolin, then use firstly a paint thats solvent / oil-based primer paint, then when dry, apply a solvent / oil-based topcoat, oil-based takes longer to dry but is kinder to wood grains & is more water repellant & it gives screws bolts & nails good protection, unlike water based paints.
Ideally, you'll need some sort of overall cover, a gazebo or similar sort of thing as to cover most if not all of the layout from rain, but something more robust & stable to protect from high winds, a wooden lean-to maybe ? A 7ft x 3ft x 6ft high lean-too made from 4"x2" tanalized CLS timber open framed with sloping roof , dessign & building this yourself works out to be stronger more suitable & cheaper than a 6ft x 4ft shed, I built a smaller lean-too for storing my garden furniture etc.
It all depends what size your layout is.