Learn Hardcore Korean: yeongyangeul saenggakhaeseo yojeum bame gwailman meogeo. - I’ve been eating only fruit at night these days, thinking about nutrition.

영양을 생각해서 literally means “thinking about nutrition” or “considering nutrition.”
Grammar-wise, it’s N(을/를) 생각하다 + -아서/어서, so it works like “because I’m considering X / with X in mind.” It sets the reason/motivation for the second clause (먹어).

Why is 영양을 marked with -을?

생각하다 commonly takes a direct object with -을/를:

영양을 생각하다 = “to think about/consider nutrition”
So 영양 is what’s being considered.

What’s the difference between 생각해서 and 생각하니까 here?

Both can mean “because,” but they feel slightly different:

생각해서: “having considered…, so…” / “with … in mind” (often sounds like a planned choice)
생각하니까: “since I think…, (I realize that)…” (more like a reason that comes from one’s thought/opinion)

In this sentence, 생각해서 fits well because it sounds like a deliberate decision about diet.

What does 요즘 modify—밤에 or the whole sentence?