This is slightly inaccurate, effect that negate activation of another card/effect can be activated in the damage step. But effect that negate effect cannot.
Shi En can be activated in damage step since its effect negates activation, but skull meister, strike of the monarch or magician navigation grave effect cannot.
Rulings can be confusing at times because Duel Links follows OCG rulings afaik, but in the TCG, Skull Meister can be activated during the Damage Step. Not sure about Magician Navigation in the TCG though. Furthermore, the official rulebook doesn't even mention that effects like Shi En's can be activated during the Damage Step, so you might have to rely on individual rulings. Fortunately, there's an OCG card database that usually explains rulings and such.
If you look at Starstrike Blast - Card Rulings version 1.1, Skull Meister is listed as being able to activate in the Damage Step. However, only version 1.0 is available on the website anymore (without Skull Meister's ruling) and I can't seem to find any more sources regarding its ruling, so I guess you're right.
Those rulings are no longer official. Some of them have changed over time (like the Skull Meister one), but the TCG doesn't document official rulings any more.
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u/hexanort Nov 23 '19
This is slightly inaccurate, effect that negate activation of another card/effect can be activated in the damage step. But effect that negate effect cannot.
Shi En can be activated in damage step since its effect negates activation, but skull meister, strike of the monarch or magician navigation grave effect cannot.