Crossbow is not rare in sengoku japan as some of it were imported from the chinese mainland, its just the warriors prefers their lighter traditional bow
Crossbow are heavier and require more maintenance than the bow, thus the preference to the bow which can be carried easily thru the mountains and on horsebacks
We should not compare the crossbow to musket, thats a totally different degree of weapons. It should be compared to the bow in the sense of time and place