Sec 44 ADA

Not allowed,

Prior to finance act 2016, proviso to subsection 2 of section 44ad provides specific deduction for interest and remuneration u/s 40(b) out of presumptive income.
In finance act 2016, above proviso has been omitted, then onwards sec 40(b) expenses not allowed out of presumptive income.

And 44ADA has been inserted in finance act 2016, while inserting specific proviso not been incorporated. So we don't have specific provision to claim 40(b) expenses as a deduction out of presumptive income.

Is there also amendment in sec 44AE regarding this..?

Not amended, 40(b) is allowed as deduction for 44AE