I was looking through a few old threads and it seems that sengoku era armies had a pretty low number of archers, even before muskets became wide spread.

That's not true. If you look at the dates given for various data point we have, you'll notice that all post-date introduction of the gun.

While we don't have the musters or legislation for earlier times, we know that prior to the introduction of the gun archery caused most of the wounds. So while we don't know the exact portion of archers present (we don't know for the time period we do have data for either mind you, we have no idea how representative our muster data is) we do know there were enough of them to cause most of the casualties. Of course that includes mounted archers.

Why is that? Were sengoku era archers not effective the way english longbows were?

According Thomas Colan, Japanese archery could only penetrate a samurai's armor under 15m range. That doesn't mean archery were ineffective (see above). However, the prevalence of armored, mounted archers must have decreased the reliance on foot archers. In pitched battle, traditionally men on foot less organized and without group drilling would be far less effective than their mounted counterpart. If generals would try to make their men as effective as possible, then we need to remember that it was far easier to give the men on foot spears and pikes, give them some basic drills, and throw them into battle. It would take far more time and effort to teach them to shoot a bow accurately and effectively. Not to mention bows and arrows were also costly to make. And the Onin War proved that men on foot with spears and pike could throw back the mounted samurai, even when outnumbered. So it's not surprising that most of the men on foot would've been armed with polearms.

Having said all that:

• As demonstrated above archery (included mounted archery) we can see were effective
• Thomas Conlan notes that outside of pitched battles, narrative sources suggest foot archers likely played big parts in skirmishing in rough terrains. Not to mention sieges.
• After his famous defeat at Nagashino, Katsuyori ordered his vassals to bring more guns, but also said they could bring bows if they couldn't bring guns. In other words, the importance of putting shot into the air was well recognized, and bows were regarded as being able to act as an inferior replacement to guns.
• This was not that much different than Europe. The largest group of combatants on foot in the 15th and 16th centuries were likely men equipped for close-quarters combat, likely with some sort of polearms. Remember this was the age of the Swiss and German pikemen.

Also I while I am not sure what you are thinking of exactly, I do want to note that the longbows, while effective, were not as effective by the 15th century as popularly depicted. You can read about that here.