Short answer: not necessarily. It depends on your itinerary and which direction you're heading.
If you're starting your charter in Lefkas town or nearby marinas on the east side of the island and planning to sail south toward Kefalonia, Ithaca, or Zakynthos, you won't touch the bridge at all—that's all open water [1]. Same if you're heading to anchorages on Lefkas's west coast; you can sail around the island entirely.
The bridge only matters if your route takes you north from the central Ionian toward Paxos, Corfu, or the northern islands [2]. That's when you'd need to pass through the Lefkas Canal, which runs on the hour openings. Even then, you have options—you can sail around the west coast of Lefkas instead, though it's more exposed and adds time to your passage.
Here's what catches people out: they plan a leg north without realizing the bridge's timetable, then find themselves stuck waiting or forced to backtrack. I'd recommend checking your planned route against the canal's schedule when you're doing your itinerary. If you're only heading south or staying local to central Lefkas, forget about it entirely.
Lefkas is an island separated from the mainland by a shallow lagoon—the bridge and canal are just one passage option, not a required checkpoint for every charter. Your boat's home port and your intended destination tell you whether you even need to think about it.
Want to work through your specific route? Let me know where you're based and where you're heading, and I can tell you definitively whether the bridge applies to your trip.