I'm creating signage for "Long-term Ventilation Unit" and am keeping it as how I just wrote it. But when Googling, I became slightly confused on whether it is "Long Term Ventilation Unit" or the way I wrote it is just fine.
Compound adjectives can be hyphenated to remove ambiguity, or open when there is no ambiguity.
The potential ambiguity is that you have a "Long Term-Ventilation Unit": a long unit for ventilating terms. Since that seems improbable, the meaning is far more likely that you have a ventilation unit available for a long term.
However, all ambiguity can be removed by adding the hyphen in the right place. It's not wrong.
Here, "Long-term Ventilation Unit" looks right; "Long term Ventilation Unit" is occasionally seen, but that can be a bit ambiguous.
The Main Point is that "long term" has adjective "long" acting on "term", whereas "long-term" is itself the adjective acting on the following noun.
Hence, "long-term" is right in your case.