Yes, rectangular pads are usually an indicator of pin position. Through-hole part footprints sometimes make pin 1 rectangular and the others rounded, so you can identify this without a silkscreen print.
Each pad in that board IS essentially a via. Termed a "thru hole" these provide a hole for the part lead, and the hole has a copper wall just as the layers do, as they are created (plated) at the same time.This is two layer PCB board. There may be vias inside the pads so do you see the vias anywhere on this PCB board?