The simple solution is:

1- Prop the stern of the boat up on a sawhorse or something similar, with the hull upward.
2- Drop the skeg so you can access the cable.
3- Run water into the skeg box.
4- Work the Work the skeg control back and forth to help flush out any salt/grit.
5- Drip cable lube down the cable and into the housing.
6- Work the skeg control back and forth to distribute the lube.
7- Repeat until there is evidence of the lube at the control end.

That's what I've done, the few times it's been necessary. I do make a point of giving the skeg up/down a good workout every time I'm on the water, though I don't think much water actually finds its way into the cable tube on the average paddle- even in the Frej where the aft deck (skeel location) is quite low to the water.

Also, it's not easy to detach the housing in some skeg systems, so you wouldn't be able to attach the tool anyway.

I was wondering if i was the only person who had built a skeg where the tube wasn't easy to remove!
:-)

Also, unless your cable skeg system has a 'friction/tension control' of some kind, you do need some friction to keep the skeg 'up' or partially deployed. so don't go too crazy with the anti-friction treatment! ;-)

Off topic:
I guess this discussion points out some advantages of 'rope control' skegs?
I've never used one myself.
There are details online (check Bjorn Thomasson's site for some ideas).
Most rudders use a rope up/down control, some working against a spring, some with a double (pull-pull) line loop.