Seedlings in shallow pots will still develop the same tap root but it will just grow sideways across the bottom of the tray. Deep or shallow you'll still need to root prune at some stage.
I usually sow seed in shallow trays then transplant seedlings into individual pots when they are large enough to handle but seed planted in individual post or deeper pots will still grow and can be transplanted and root pruned when you are ready. Some seedlings get left in the shallow trays for a year or 2 because I don't always get time or space to transplant them all. Transplants to individual post usually grow faster due to no competition but no real drawbacks with either way.
Trees tend to grow faster and bigger in deeper pots, probably because of more stable moisture, temp and nutrients in the deeper pots. Shallow pots can dry out very quick in summer so be prepared to water often, especially if you have lots of seedlings all trying to grow and using up water from the soil.
Both shallow and deeper can be used. Both have advantages and disadvantages so it probably comes down to individual preference.