Osquery uses basic SQL commands to leverage a relational data-model to describe a device.

osquery

if I run an on-demand query (via fleetctl or web ui) and some of the endpoints are offline, the query will be run when the machines come online, or I just lost some host results?

you won't get those results. that's why the query web UI will have the number of hosts targeted next to the number of hosts actually responding, so you can tell

if there's something you need from hosts that aren't currently online, save it as a scheduled query and check back in later

yes, I will add the query in the scheduled queries. Thanks