My mother's I-94 expires on 1/5/15 and I'm looking to see if she can leave at 1/6/15. Her flight will depart 5 min past midnight on the 6th , however, she'll check in at the airport around 10pm. Would she be out of status?

Isn't it kind of early to be checking this if she doesn't depart until January 6th, next year, at past midnight. Or are you posting the wrong year ? But yes, a day later does make a difference. Cant you get her there on the correct date and time ?

I am checking for 2015 because I want to make sure that she's not going to be in overstay status. The flight is super expensive on the 5th, but is very reasonable on the 6th, and that's why we are trying to figure out if she will be out of status if she leaves at 5 min past midnight and cause her to have problems when she comes back for visit in the future.

Yes, she will be out of status, and yes, she will accrue 1 day of unlawful presence. The only definite consequence is that the visa she entered on will be void (if it isn't expired already).

"cause her to have problems when she comes back for visit in the future" is so vague and circumstantial that it's impossible to answer. U.S. consular officials can and often do give people "problems" when they want to visit whether or not they have overstayed.

File for an extension of status prior to the expiration of her I-94 and she will be in status with the planned departure. You will need to see if the I-539 filing fee is worth the "overstay" on her record.

Good luck!