I assume OP's initial At least we will come to isn't at issue here, so let's reduce #1 to...
1: ✳ We know that how many trees are exist in the town.
Where ✳ denotes "unacceptable to native speakers". (I've also removed the syntactically invalid that, capital Trees, and quotes around "are").
The reason #1 is an invalid construction is because are and exist are both finite verb forms performing the same syntactic function (approximately, that of a copula linking trees to in the town). We can make it grammatical by removing either word,...
1a: We know how many trees are in the town.
1b: We know how many trees exist in the town.
...or by replacing exist with an adjectival form, giving the starchy/formal, but perfectly valid...
1c: We know how many trees are extant in the town.
Note that in principle we could replace exist with a continuous participle, but idiomatically we wouldn't normally use are existing (probably because of the semantic overlap between to be and to exist). Though there's nothing unusual about, say,...
1d: We know how many foreigners are living in the town.
I'd guess to be is the most common verb in English (because of its use as an auxiliary), but we don't actually use it very often as a "true" verb in the sense of to exist. It's just that some examples ("To be or not to be" and "I think therefore I am" come to mind) are particularly well-known.
TL;DR: If the intended meaning is to exist, use that verb. You won't go far wrong if you only ever use to be as an auxiliary verb,