If you declare an item and it turn out to be illegal would you still get in trouble at customs ?

"Illegal"?  How does a THING become "illegal"?   You mean illegal to import, illegal to possess, illegal for YOU to possess, illegal under state or federal laws? Illegal under local laws?  Technically, you could argue that your possessions are not under local jurisdiction until you pass through customs. However, it might be foolish to try that if you might have to cross outside of customs to reach your connecting flight.

If you declare an item that turns out to be in excess of the exempt amount for duty-free import, they will simply assess the duty owed. If it is an item prohibited by state or federal laws, they may confiscate it until you can prove it's not prohibited.

I have worked with people who failed to declare things that they KNEW were legal, and yet they were still arrested when customs agents felt otherwise. For instance, re-importing a $40,000 portable computer made in the USA and failing to "declare it" because it was owned by a federal agency.  Oops.   Should have declared is as "exempt", not "smuggled".

Depends on what it is

Illegal drugs you get in trouble

A vegetable that is not allowed it gets confiscated and you get a warning

You very well may, yes.

You could still get in trouble for it.

Illegal is illegal. Admitting you have it doesn't change that. 

You can, yes.  

I knew a lady who carried an electronic "stun gun" for self defense.  It was legal to carry in her home state and she took it with her on a trip overseas.  On her return trip she connected through JFK Airport and was asked by a customs inspector if she was carrying any "contraband or weapons."

Not knowing stun guns were illegal in NYC, she told the agent "just a stun gun in my checked bag."  The agent searched the suitcase, found the stun gun, pulled her out of the inspection line and handed her to NYPD.

She was charged with possession of an illegal weapon and held in jail for nearly two days until her lawyer back home negotiated her release on bail.  She ended up accepting a plea deal for a reduced charge that required a fine and unsupervised probation.

This was over 15 years ago and as of 2019 she says it still appears as a "blip" on her record when returning to the USA. She has been pulled out of line for "additional screening" at all but one U.S. airport when returning from an overseas trip.

Most times no..unless you knew it was illegal