Quick update for anyone reading.
I must apologise because after additional testing it was the Ubuntu UI theme that was causing the issues I saw.
It turns out that PDI 9.0 can work reasonably (if you are just using Spoon and Carte) without libwebkitgtk-1.0-0. The only noticable difference is that the Welcome screen on opening opens in a broswer rather than in spoon itself and some help pages don't function.
I successfully removed all the 'old' packages above and a simple Theme change (back to default from Dark/Light) meant the UI elements were visible.
Thanks for you help anyway.