If I recall rightly, hydrogen leaks out of the balloon so fast because of the change in pressure at high altitudes. Not a problem at lower ones, but way up I seem to recall that it is.
Funny because helium leaks out faster than hydrogen under regular conditions, being smaller in practice.
Methane has a decent amount of lift, it's relatively cheap, and it stays in the envelope.
This is an unmanned device so it doesn't have the same safety concern. Also at the cruising altitude there is so little oxygen it's probably as safe as helium at that altitude.
Sorry, maybe it wasn't obvious enough the first part of my comment was intended as a joke?
In Australia we use hydrogen in our weather balloons. It’s essentially a safety/cost trade-off.