Why are phylogenetic trees considered hypotheses?

They are considered hypotheses for a few reasons : Evolution of organisms has been occurring for hundreds of thousands of years.Since no one has actually been around that long to observe exactly what happened, phylogenetic trees are based off of 'clues' we have such as the fossil record and mutations in mitochondrial DNA. Therefore the 'proof' we use to make phylogenetic trees is not necessarily solid 'proof' but is instead facts put together through strong correlations.

If it doesn't have a nucleus its a prokaryote

Average growth population growth