SAN DIEGO — The third try was the charm. The Padres, who already had two shortstops, got their shortstop. Shortly after the Winter Meetings ended, the team and free agent Xander Bogaerts reached an agreement on an 11-year, $280 million deal Wednesday night. That came after the Padres’ unsuccessful attempts to land shortstop Trea Turner on Monday and right fielder Aaron Judge on Tuesday. Bogaerts will almost certainly play shortstop for the Padres in 2023 with Ha-Seong Kim moving over to second base and Fernando Tatis Jr. playing in the outfield when his suspension for a failed PED test is over…