There's a fine line between the homoerotic and the homosexual. Whenever you have a culture where all important relationships are between men, and where women exist on the margins of male life to provide domestic service, bear the next generation, and scratch the old sexual itch, there is possibility that men who share a deep emotional intimacy will express it sexually. Sometimes they do, as in classical Greece and among modern day Pashtuns. Sometimes they don't, as (for the most part) among 19th century upper class Anglo-Saxons.

As for David and Jonathan, like Achilles and Patroclus, the contemporary author hasn't put them in bed together. Our own predispositions, religious and otherwise, lead us to resolve the resulting ambiguity as we would like to. And I wouldn't be as certain as you seem to be about the mores of the Biblical Hebrews c. 1000 BCE. The Bible wouldn't be quite as vehement as it is on the subject of homosexuality if it wasn't a real phenomonon.