You’ve said before that ex-hosts in Eleutherophobia can have blunted affect such as their expressionless speech. Does that still happen when Tom uses thought-speak, which doesn’t require any physical muscle control?
So. My headcanon about thought-speak is that it doesn't have tone like voice-speak, but that it does convey emotions in its own way. For example, in MM3 Rachel notes that Cassie's thought-speak "was alarmed. She'd heard the guns. But she didn't know... about Jake." Later, when discussing the Holocaust, Ax notes Rachel "[thought-] spoke with no special emphasis. No anger."
If Rachel can tell that Cassie a) heard gunfire but b) doesn't know Jake is dead, then Rachel has a pretty good read of Cassie's mood just from the way Cassie shouted the word "What?". Definitely more information than Rachel would've gotten from Cassie texting her the word "What". Ax noting Rachel's lack of emotion in thought-speak also suggests she normally does have emotion coming through.
Based on what we see in #1 and #33, thought-speak can convey a lot of things voice-speak cannot: images, memories, a sense of someone else's emotions in your own body. But it doesn't necessarily convey tone. We don't see any instances of characters being "shrill" or "hoarse" in thought-speak, even though those are common in voice-speak. In #50, Timmy has trouble generating language, but can use thought-speak fluently. So it's not like talking on the phone.
I headcanon that is why no one can tell when Ax is joking: In andalite-to-andalite communication, intent is obvious by default, so you'd never need to lower and sharpen your voice to get verbal irony across. Galuit can't tell when Jake is being sarcastic (#18) for the same reasons Jake can't tell when Ax is being sarcastic; there are two different ways of conveying it. Ax is like "obviously I willed a certain ironic distance into my words; why is that so hard for humans to understand?" and the humans are all like "bro, when using mouth-sounds you gotta inflect irony."
As to what that all means for yeerk hosts, who sound "flat" (#45) and "slurred" (#2) when talking out loud... Hm. Gotta think about it more.