I can’t say enough about proper fitting orthotics. I too wear them and there are certain activities I cannot do without them. I recently had my 7 YO fit for them as well to correct his pronation. I took him to the doctor because he periodically complains of having a sore back (at his age!). There was nothing major going on, and he hasn’t been injured, so we’re hoping with proper alignment his back will stop hurting. Don’t know yet, just got them last week.
Fixing the pronation via orthotics can help with proper alignment of the entire skeletal system starting at the feet and ankles and moving right on up to the knees, back, neck, etc. Makes sense, it's all connected. There is a very good possibility that proper correction now can help with your child’s ankle pain, not to mention other aches and pains that could crop up in the future from improper alignment.
Because orthotics can be very uncomfortable at first, you could try breaking in your 3 YO gradually with a softer, less rigid, EVA material. Most Podiatrists recommend a hard, rigid plastic. Speaking from personal experience, I DON’T recommend it for an orthotic newbie, especially a little kid. Many adults can’t even tolerate them and hundreds of dollars end up in the garbage. If the hard rigid plastic is recommended, maybe your child could graduate to them eventually.
You’ll have ample opportunity to make changes to the orthotics, as it’s been recommended to me to have my son’s replaced every 6 months (will vary by growth spurts), so you’re not stuck with them for years. I only recommend this because if they’re too uncomfortable from the get go, they will not wear them, or will do so with extreme resistance (tantrums, etc.). Older kids will just remove them and not tell you.
They will notice the new orthotic no matter what and there should be a break in period (my personal opinion - don't go on a long hike on day one and get break in instructions from the Doc or orthotic mfg). The only word I can think of for a new pair of orthotics that are providing some correction or support is, annoying. The more the correction, or support, the more annoying. So, I guess you're looking for that point of tolerance until they get used to it. It took my son a day to get used to them and he hasn’t mentioned it since.
Hope I didn't write too much.