My wife got her periods on 25th July and on 6th August we had unprotected sex followed by an ipill which she had in 4 hours after the act. On 7th August we had protected sex 3 times with new condoms for each act and after each act she washed herself with water.

13th Aug she had bleeding like her periods but less flow(60% bleeding, considering 100%bleeding during her normal periods), no pain, with very few clots(1-3 clots instead of 8-9) and it was there for 3 days almost(on and off). Her periods were due on 25th Aug (she has irregular periods sometimes).

We did a home pregnancy test that week with negative result and did the second pregnancy test on 5th Sept again with negative result.
We also did UPT in Lab with negative result on 14th Sept.
She has no symptoms of pregnancy.
Its 16th Sept she has not got her periods yet.
Is she pregnant? 

The morning after pill ( which is for emergency, not normal use of planned sex) can cause a women to have off or even no periods for one or two months. (read the warnings) along with many other side effects.

With that said, it is also to early to do pregnancy tests.
It also could have just been a light period, women's periods vary from time to time.

At this point it sounds more like the effect of the morning after pill.

But.
The morning after pill is not 100 percent effective.
Condoms have a 3 to 18 percent failure rate.
False negative pregnancy tests are common.

So could she be pregnant yes. At this point, you wait till this months period is due and see if she has it.

Most likely not pregnant since she took I-pill and she had a negative pregnancy test 5 weeks after the unprotected sex. Since she has irregular periods sometimes, you may want to test again in another week or two and see what the results are for the peace of mind.