"I'd like to know what's the difference between "come in on weekend "and "come in on a weekend"?"
The first is very informal - I'd call it bad English - for "come in on A weekend" or "come in on THE weekend". It depends on the context of the preceding conversation which one is meant. Not only is it potentially confusing, but it doesn't sound very good.
However, you will hear the plural, as in "Can you come in weekends? and that is standard and common. Often it's the question asked by an employer if they want someone to come in to work on Saturday/Sundays for a period.
And yes, a weekend is a Saturday and Sunday. (not a Saturday OR Sunday)