Whenever you notice unnecessary margin/padding in the Top Bar, where the logo, menu items, cart, etc are, and want to decrease it or remove, make sure you did not set too large value for the logo height under Betheme > Theme Options > Global > Logo > Advanced section. Top Bar size depends on the logo height and if this value is too big, you will notice empty space especially above and under logo and menu items.
If above field is empty, the default height is 60px. To get rid of the default padding around the logo and rest of elements from the Top Bar, please type 0 into field.
There is also another option below height, Vertical Padding. Thus, if above did not helped, please leave this field empty or set its value to 0 too.