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In Disney canon, the Sith use dark side energy emanating from the Sith shrine beneath the Jedi Temple to cloud the senses of the Jedi, allowing them to hide in plain sight. No particular Force power is used.
However, this isn't known to modify one's midichlorian count. Tests for midichlorian counts are part of the standard medical checkups in the Galactic Republic. Why isn't Palpatine found out during any of the routine medical checkups a government official would have to go through?
A high midiclhorian count doesn't necessarily mean that the person is strong in the force or even force sensitive they state that in The Phantom Menace. And Palpatine was a member of an aristocratic Naboo family, his father was a very influential man. And although it isn't Cannon the novel Darth Plaugeis shows that Palpatine's father had no love for Jedi or force users in general. So even if Palpatine was tested as a child his father probably would never let any of his children become Jedi and any time after that wouldn't matter. He would be to old and never would have been allowed into the order.
I definitely have read a comic which explained this (although i'm pretty sure it wouldn't be canon anymore). I thought it was in the Clone Wars volumes of Star Wars: Republic but I looked up the summaries and I might be wrong - maybe it was in one of the Legends? anyways.
Somehow the idea that there is a Sith in the senate is presented to the Jedi council, and somehow Anakin finds out. He and his master (I believe it was Ki-adi mundi at the time, as Obi-Wan was being held captive by Ventress?) run the idea by Palpatine, because Palpatine and Anakin have some sort of closeness, who suggests that testing all senators for midi-chlorians would have grave political consequences (which makes sense from the Jedi's perspective).
IIRC, either Palpatine organizes it so that the Jedi who was championing the cause was sent on a mission where the military intelligence underestimated the droid forces by an order of magnitude and died, or he arranged for a transport vehicle for the senator championing the idea to explode leaving Coruscant as Mon Mothma and Bail Organa watch horrified, and then something else comes up that takes the attention of the Council.
This is a bit vague cause it's been years since I read these, but this was the canon explanation pre-legends.
Easy, the dark side is the art of deception. If a midichlorian count was performed on Palpatine, he could easily cause the the person administering the test to forget the exact number and write another one down.
