In the following sentence (from here),
I would have expected です instead of あります: 広さ = ５０００m²以上.
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is a perfectly natural-sounding sentence.
「あります」 can be replaced by 「です」, but that will change rather drastically the basic grammar (if not the meaning) of the sentence.
In the original sentence, 「５０００m²以上」 functions adverbially to modify the verb phrase 「あります」. As discussed in this Q&A, number-related phrases can function adverbially in Japanese. From my own experience with Japanese-learners, however, they seem to have difficulty getting used to this concept.
It is more natural (or more "originally Japanese") to say:
「リンゴがむっつあります。」 ← 「むっつ」 functions adverbially.
than to say:
「むっつのリンゴがあります。」 ← 「むっつの」 functions adjectivally.
Thus, in the sentence you were thinking of:
「５０００m²以上」 functions as a noun.
In this sentence there is no difference in meaning between です and あります. But あります sounds politer.