Joists have different height
Dimensional lumber when green can vary in size depending on the day it is cut as it dries it gets worse because some beams are tighter grain than others. Since you have good access you could shim the areas that have the squeak with wood shims. Put some gorilla glue or wood glue on the shims and slide 1 in from either side. Don’t drive them in two far or the squeak will move. This is normal for dimensional lumber joist. Many builders now use LVL I beams to create a squeak less floors. By taking a few hours and shimming the gaps your floors will feel solid and the cost is minimal.
If you screw down without the shims the problem will get worse and your floor will show the uneven surface.