While I am not going to say it never happened, if it did it was rare beyond rare. While any polearm except the Naginata (which counts as a bladed weapon, or "katana") is called a yari, for the most part the yari is a two-handed weapon so while there are many types of yari they are pretty much all very unsuited for throwing. Given how well-established archery was already when ashigaru became widespread in the Sengoku, and the quick taking up of the arquebus after it was introduced, any thrown spear would have been hard to compete with them. If they wanted to throw something, they threw rocks.

Due to the wide variety of types of yari, the methodology would depend on the type. It seems though for the shorter (still two-handed) mochiyari and the longer what we'd call pike, the suggested primary method seem to have been fencing and bashing, trying to knock down the opponent's weapon and also hit him. Thrusting is said to be a single-combat tactic, so in group-combat is probably only used when there's an opening. When facing mounted warriors, it's also suggested to thrust at the horse's stomach first before trusting at the fallen rider.

Also, various variations of a cross-shaped tip was popular for the shorter mochiyari, which could be used to hook and do a side-way thrust into the armpit or other gaps in armor.