If I go to the map screen and click on a system a number shows up saying “X” jumps.
But, if I set that system as my destination, when I return to the main screen the Route section says a different number of jumps. Often an EXTREME differences!
Ex: I was a look at a system in Amarr space. The map said 22 jumps. But when I made the system my destination the Route said 47 jumps! 
Why the difference?
The map screen shows the shortest gate-to-gate route, ignoring all potential hazards along the way. The autopilot planner adjusts the route based on your routing settings, including but not limited to restrictions such as avoided systems (like Jita, which is always avoided by the AP system unless it is your actual destination), security preferences, and recent player death preferences.
You can edit these preferences by, IIRC, clicking on the capital A icon next to the autopilot destination and jump data.
Got it.
Yea, to do the 22 jump route, 1 would be through .4 space and 3 through .3 space. 
The map also gives you filters that allow to check for “ship kills in the last hour” and “pod kills in the last hour”.
Those two are good indicators to guesstimate if there are potential gate camps (ship kills) or smart-bombers (pod kills) along the lowsec part of the way.
You can find these filters in the map with the little cog-wheel in the top right.
If you don’t need to bring a big ship to said location, you can try getting through in something fast and cheap like a shuttle.
If you need something hauled there, you could create a courier contract for someone to move your stuff to said place. (Check the MotD of the “Haulers Channel” ingame for tips and good answers to eventual questions on how that works)
Or you could start looking for wormholes that lead you close to your location. Maybe there is a convenient Thera wormhole - but be aware that entries from highsec into Thera might be camped too.
You can check for Thera connections on: Thera Wormhole Connections - EvE-Scout and also get on the public access list for the wormhole bookmarks.
I hope that helped a bit.
Happy travelling.