Danelle Williams

Chosen answer: Did they? They are both still voiced by the same actors, so either A. you are imagining it, or B. they changed the voices slightly to make performing them every day easier.

Grumpy Scot

It's true. You can simply tell SpongeBob's voice from season 4 and onwards (in my opinion, downgradingly) changed to a higher pitch tone.

Answer: Also their voices might've changed due to their actors getting older.