Yes that is true, they do not understand magic but then again most ponies probably don't understand science just as much because they don't need to.
This is really hard since Magic doesn't exist in the Half Life lore (apart from the vortigaunts thing (Its not meant to be magic)) and because in MLP science isn't really explained (then again the same can be said about magic (magic is explained more than science)). But overall the weakness of the Equestrians is that they are mostly peaceful and that 2/3 ponies (If we say all pony races have an even amount) struggle because they have no fingers or magic, their army is useless and are mostly peaceful, the upside of the Equestrians is that they have 4 princesses and the elements of harmony and they have traveled to another dimensions/parallel time line (1 or 2 depending on weather you count the IDW comics as canon). The weakness of the combines is that they do not understand the magic of the ponies and that their foot soldiers are idiots and that they have multiple enslaved dimension/planets to focus on while their strength is that they have multiple advanced technologies and G-man and have been to multiple dimensions. At the end of the day I am pretty sure that Combine would win.
As for how long it lasts I guess about a week or two. A fun thing to do is to consider the Equestrian Civil War, if it is still going the war would last around 2 days but I would say if it has finished and a side has won or they made peace yet still had the army it would take around a year.
(I am sorry if any information is wrong, to be honest I have really looked into the Equestrian Civil War and have not read the new IDW FIM comics or IDW micro series and IDW friends forever)