Depreciation is governed by sec 32 and not 40A(3).
First of all dep. is disallowed if the following conditions are not satisfied u/s 32 :-
1) Assessee does not own the asset (except some exceptions).
2) Assessee does not use the asset in the revelant previous year.
Secondly, Sec. 40A(3) does not apply to any capital expenditure. Here the word "CAPITAL EXPENDITURE" is important.
Sec. 40A(3) applies only to "EXPENDITURE INCURRED IN CASH".
Depreciation is not an expenditure. It is just a charge over the asset - A NON CASH ITEM.
So there is no scope disallowance of depreciation under sec. 40a(3).