This question has been answered by sketchi. See the first response.
2. I've changed ms2_product_thumbnail_size in System Settings but the images on the category pages are still the default 120x90 and new images I upload are stored in the folder 120x90. Is this a bug or is it just me?
3. The default size of images on product pages seems to be 360x270 - how do I change this?
[[+360x270:default=`/assets/components/minishop2/img/web/ms2_medium.png`]]
[[+url:default=`/assets/components/minishop2/img/web/ms2_medium.png`:phpthumbof=`w=340&zc=0&q=95&f=png`]]
PhpThumbOf not needed at all.
All thumbnails are generating according media source settings when you uploads image in product.
Then you can show it by snippet msGallery (use placeholders by it size, for example [[+120x90]]) or in snippet msProducts (same placeholders, but you must to include needed sizes by parameter &includeThumbnails=`120x90`)
Also you can look at products gallery at minishop2.com/manager/, login/pass: demo/demo