Potential answer, but I can't find a more complete synopsis
EDIT: Google Books allows a limited search-inside-book feature and this is definitely the correct answer for my half-remembered book. I hope it is what Emily was searching for, too. I can even confirm that the tree-stump-alikes were called the Soshtii.
It might be Ghost Ship to Ganymede by Robert Swindells. The only synopsis I can find for that title is,
Fay, Tom and Grover stow away on a spaceship and find to their horror
that they are en route to unexplored Ganymede, a moon of Jupiter.
(from Google Books)
Well that fits, as far as it goes.
I could have forgotten a third character. Mentioning that Ganymede is unexplored is a favourable point, and sets this book apart from many others; it certainly wasn't set on a well developed Ganymede as most stories seem to be. I forgot to be clear that the lifeforms in the canyons are previously unknown, and discovered by the children.
Robert Swindells apparently writes for the right age group, too. Room 13 was also his, for instance.
I can't find a library copy of Ghost Ship to Ganymede, a download (legal or otherwise), or a reasonably priced hard copy. I can only find some that are, for whatever reason, pushing the £1000 mark.
I wonder if the synopsis rings true with Emily as well? Perhaps she could perform an image search for that title, and see if any covers look familiar?
I'll also see if I can hunt down a copy by ringing some bookshops.
Must, consolidate, early, memories! Or, might, never, punctuate, properly, again!