They did use formations. At the onset of the Sengoku Jidai, spears replaced mounted archery as the dominant form of fighting on Japanese battlefields. I don't know if you've ever fought with a spear but one on one it's a bit difficult to use at best, so formation fighting was simply better than non formation fighting. Toss in guns recently introduced by the Portuguese and you can see why fighting in formation simply made more sense. Cavalry charges were also fairly new additions to the Japanese battlefield, which made fighting in formation with spears almost necessary to deal with this new tactic, as well as the previously mentioned mounted archery. Spears needed to be able to cover guns.

I can't comment on the samurai charging into battle thing but I have a sneaking suspicion that's another samurai myth, like Bushido.

Source: Japan Emerging edited by Karl Friday

The Fourth Battle of Kawanakajima (lit. Island in the middle of the river) was known for utilizing two examples of formations: Takeda Shingen used a "kakuyaku" (lit. "Crane's Wing") formation, which was a formation that placed skirmishers (archers and arquebusiers) on the outskirts of a formation with a semi-circle vanguard of spears in the front and a narrower group of troops behind it protecting the commander. This formation could be considered analogous to the Spanish tercio, as the idea was that the skirmishers could withdraw to the protection of the melee troops in case of a cavalry assault.

Uesugi Kenshin, his opponent, tried to counter this by using a wheel formation. The idea was that he would send wave after wave of troops in a loop against one flank, thus constantly battering the same portion of the enemy troops with fresh units, in the hope of breaking through and being able to attack the interior of the formation, which would be vulnerable.