Casting a spell from a scroll is casting the spell. With the exception of the training and spell slot required to do it, and the need for the piece of paper, it’s all exactly the same.
One of those differences does matter here, though: the rogue has to be able to see the scroll to read it. So they need see invisibility or similar. Probably not a deal-breaker, but a thing to be aware of.
Does he get penalities to hide?
If the spell involves an attack, “It’s practically impossible (−20 penalty) to hide,” and at least personally I’d extend that to include any spell that clearly has something projected from the caster’s space, e.g. fireball, even if there’s no attack roll involved. (Besides, in context, the word “attack” is probably meant in its broad sense of “any offensive action that directly targets a creature,” as opposed to the narrow sense of “involving an attack roll,” though 3.5e is notoriously unspecific about these two most of the time.)
On the other hand, if it’s like summon monster or something, then no, there isn’t any visual indication of the caster’s presence, the monster just appears suddenly.
Does the scroll emits lights which would affect the hiding?
Nothing says the scroll itself does. The spell being cast very well might, though for a lot of spells that’s going to be a judgment call for the DM because the descriptions aren’t detailed enough. So like, light or probably any fire spell, sure, there’s light emitted. For summon monster, probably not, or at least nothing particularly suggests there is. But magic is often flashy and the rules just aren’t clear about it.
If the rogue casts a spell from the scroll that needs verbal components, does this mean that the rogue can be heard by other creatures?
Yes, the rogue needs to “complete” the spell, i.e. perform “the final gestures, words, and so on.” If the spell has a verbal component, completing it will involve speaking. Less or less-complicated speaking, but it will still be audible. Note that the rules specify that “you must […] speak in a strong voice” for verbal components, so no whispering is allowed.
This also means that silence or superior invisibility prevents verbal components (a fact both spells mention explicitly). On the other hand, being incorporeal, to my mind, shouldn’t block speaking—incorporeal creatures are described speaking, or wailing or shrieking or what have you, all the time. But there is no way to perform a verbal components silently—either you can speak and thus be heard, or you cannot and can’t use verbal spells.
Do targets of spells get a spot check to possibly spot the rogue/caster?
Yes—again, “It’s practically impossible (−20 penalty) to hide,” which means a new round of Spot vs. Hide, Listen vs. Move Silently is appropriate.