Hi again,
My comments are in italics.
(1) Susan puts some nuts on the chocolate cake in strawberry sauce, which are her favourites.
1a- Is "her favourites" referring to "some nuts"? Is it clear in meaning? Any other possible meaning? In theory, it could also refer to the two items, chocolate cake and strawberry sauce. It'd be clearer to put the relative clause immediatley after the word 'nuts'.
(2) Susan puts a cherry on the chocolate cake in strawberry sauce, which is her favourite.
2a- Could "her favourite" refer to "a cherry"? No
2b- Or, is "her favourite" will still inclined to be 'chocolate cake in strawberry sauce' as it is the nearest words to "her favourite". Yes
2c- Could it mean "her favourite" = "a cherry on the chocolate cake in strawberry saurce"? Very unlikely if not, how to present for that meaning? I think that for clarity, you'd have to be explicit. Perhaps say something like 'which is her favourite combination of three things'.
2d- If "her favourite" is just "the cherry", then "Susan puts a cherry, which is her favourite, on the chocolate cake in strawberry sauce." Right? Yes, yes, yes.
2e- If "her favourite" is just "the cake", then "Susan puts a cherry on the chocolate cake, which is her favourite, in strawberry sauce." Right? Yes
2f- In general speaking, is it not proper to make such an unclear sentence? Any exception? It depends on what you mean by 'proper'. To tell you the truth, if you say this kind of thing to me, I just smile because you're friendly, I smile back, I say 'That sounds nice', and I don't much care exactly what you mean.
Best wishes, Clive