Are adjectives with the prefix "non" considered compound adjectives? For example, non-profit or non-biodegradable.

I'd say yes.

A compound adjective is comprised of more than one word, usually hyphenated. Examples: well-behaved four-foot all-too-common See grammar-monster for more examples.

However, note that in some dictionaries the adjective (compound or not) non-profit might appear as nonprofit, where the negation prefix is not hyphenated.