I'm married to a USA citizen since 2009 but when on my visa application I put married to my ex-wife in my country.

Consult with an attorney in private as the consequences to misrepresentation can be severe.

CAN YOUR CHILDREN(US CITIZENS)APPLY FOR YOUR GREEN CARD I YOU WERE BEING DEPORTED BEFORE

I would consult with attorney and do a FOIA for your full history. Likely not due to second deportation after illegal entry, however worth review.

Would Trump's EO on H1B only impact future H1B applicants or would it also impact H1B visa holders with approved I 140s?

There is no EO re: H1b nor is there any suggestion of such. I would continue to stay updated or meet with an attorney to discuss your situation...

Avvo is a good source to find attorneys. Also contact your local shelter/DV clinic as they will probably have contacts as well.

How likely is to get a green card after a U visa for 3 years.The case has not being prosecuted. What immigration will look for?

There are other factors to consider such as whether you will need a waiver for any ground of inadmissibility. I recommend contacting an attorney to...

Can a spouse of a green card holder do the adjustment of status process?

Yes and refer to Visa Bulletin for priority date info.

Immigrant visa petition for wife in Pakistan, delayed more than 60 days.

If you have submitted all requested docs there is not much more you can do but wait for an interview date. NVC will contact you otherwise. You can...

Should I apply for I-90 renewal?

Probably not but I would advice speaking with an attorney so that your file can be reviewed more thoroughly.

First acquire a divorce attorney to assist with the divorce and once you have done so can apply either through your current USC spouse or a VAWA...

You should not have any issues and should consider the option of applying for citizenship.