"Das All sieht schwarz aus."
I wouldn't say 'looks' and 'appears' are ever perfect synonyms. Both 'appear' and 'seem' imply a sense of doubt: a phrase like "He seems [honest]" might be followed by something along the lines of "but in fact [he's a professional liar]". There is definitely a sense of incertitude/doubtfulness/tentativeness implied by these verbs. 'Look' on the other hand has a more objective feel to it, as it is generally grounded in visual evidence: "It looks like it's going to rain" = "I'm pretty sure it's going to rain [judging by the dark clouds]".
I think 'aussehen' holds some of the visual implications of 'look', whereas 'scheinen' suggests the doubt connoted by 'appear'. To answer your question, it makes sense to write something like "Das All scheint leer zu sein" (The universe seems to be empty), given that we suspect it is not so.
My native language is neither English nor German, so I'm looking forward to feedback from both camps on this subject.
I would say that 'looks' and 'appears' are perfectly synonymous. What you described is the difference in meaning between 'seems' and 'looks'.
To me the semantic difference in this context between the latter two verbs is a rather subtle nuance, which is why I originally suspected that 'seems' might work. Nevertheless, your point is certainly valid and helps clear it up for me.