Nouns, whether concrete or abstract, are very often used with "without".
Supper without you tonight, a melancholy prospect.
— Marilynne Robinson, Gilead (sentence fragment)
Your first example reads better because the parallelism is clear. For the second one, I would prefer:
Analysing without deeply understanding the science is pointless.
However, even this is not as good. The abstract noun "analysis" works well on its own, but the transitive verb/gerund "analyzing" feels incomplete for lack of an object.
I also added "the" before "science", which yields the meaning "whatever science is relevant to the analysis" rather than suggesting you somehow have to understand all of science. An alternative solution would be "how science is carried out" or "the scientific method", according to what you mean.