Spell Combat I think is the important bit. The archetype alters spell combat (and does not replace it) in some specfic ways so lets see.
The normal ability reads as follows:
At 1st level, a magus learns to cast spells and wield his weapons at the same time. This functions much like two-weapon fighting, but the off-hand weapon is a spell that is being cast. To use this ability, the magus must have one hand free (even if the spell being cast does not have somatic components), while wielding a light or one-handed melee weapon in the other hand. As a full-round action, he can make all of his attacks with his melee weapon at a –2 penalty and can also cast any spell from the magus spell list with a casting time of 1 standard action (any attack roll made as part of this spell also takes this penalty). If he casts this spell defensively, he can decide to take an additional penalty on his attack rolls, up to his Intelligence bonus, and add the same amount as a circumstance bonus on his concentration check. If the check fails, the spell is wasted, but the attacks still take the penalty. A magus can choose to cast the spell first or make the weapon attacks first, but if he has more than one attack, he cannot cast the spell between weapon attacks.
Eldritch Archer has the ability Ranged Spell Combat which states:
Instead of a light or one-handed melee weapon, an eldritch archer must use a ranged weapon for spell combat. She doesn’t need a free hand for ranged spell combat. The eldritch archer cannot accept an attack penalty to gain a bonus on concentration checks to cast a spell defensively.
This ability modifies spell combat.
by the RAW the altered text should read:
At 1st level, a magus learns to cast spells and wield his weapons at the same time. This functions much like two-weapon fighting, but the off-hand weapon is a spell that is being cast. To use this ability, the magus does not need to have one hand free (even if the spell being cast does not have somatic components), and must use a ranged weapon. As a full-round action, he can make all of his attacks with his melee weapon at a –2 penalty and can also cast any spell from the magus spell list with a casting time of 1 standard action (any attack roll made as part of this spell also takes this penalty). A magus can choose to cast the spell first or make the weapon attacks first, but if he has more than one attack, he cannot cast the spell between weapon attacks.
Some of the language doesn't make sense however, and it's reasonable to adjust or remove statements that don't make sense. Unlike the Myrmidarch, the eldritch archer does not have the option to use a melee weapon. So, lets remove anything that talks about melee weapons since this flat out isn't an option the eldritch archer has. This changes things to read:
At 1st level, a magus learns to cast spells and wield his weapons at the same time. This functions much like two-weapon fighting, but the off-hand weapon is a spell that is being cast. To use this ability, the magus does not need to have a free hand (even if the spell being cast has somatic components), but he must use a ranged weapon. As a full-round action, he can make all of his attacks with his weapon at a –2 penalty and can also cast any spell from the magus spell list with a casting time of 1 standard action (any attack roll made as part of this spell also takes this penalty). A magus can choose to cast the spell first or make the weapon attacks first, but if he has more than one attack, he cannot cast the spell between weapon attacks.
It seems that the answer to your question is yes, they do still take a -2 penalty to the attack. Some points on this.
*Two Weapon fighting doesn't specify attacks must be made with melee weapons. So, the text referencing two-weapon fighting makes sense to leave in. This means there is still a basis for the -2 penalty.
*Even if you decide Two Weapon fighting only applies to melee weapons and therefore should be removed, I would draw your attention to the feat Rapid Shot. Which is the two-handed ranged weapon equivalent of two weapon fighting. Like Two Weapon fighting it grants you an extra attack, but at the expense of a -2 penalty to all of your attacks.
Sure, it sucks that you lose your spell if you miss, but the real tradeoff is that you're not in melee.