I have a lot of canoes and kayaks and wouldn't use a trailer for all the negative reasons already stated.
One thing to consider if your hatchback is hitting your kayak. You can try to raise the yak higher off the roof.
You can raise the bars higher off the roof with some systems by using taller towers, if available. Extra tall towers used to be available from Thule if you used their false gutter mounts.
You can also lift the hull higher off the bars if you attach foam blocks, saddles or J racks onto the bars and into which the hull will rest.
Canoe/Kayak Storage Racks
Dock & Launch Systems
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