The concept of randomly generated "wandering monsters" has pretty well gone out of use. However most adventures include descriptions of monster/enemy daily routines which will give one an idea of when something or someone might be patrolling the area the pcs are trying to camp in.
When Im running a campaign and the party elects to camp in hostile territory (inside the dungeon per se), you better believe I have a good idea of what will be actively hunting or patrolling in that area and how often it might come by the camp site. Not so much "wandering monsters" as "hunting or patrolling monsters".
On the magic vs skills debate in theory magic trumps skills in flash (bonuses and the ability to avoid situations that result in skill checks) but a skilled character is much harder to counter. Many defensive tactics and spells can effectively neuter a caster-scout while a skilled on will be only inconvenienced. And yes being invisible gives you a +20 Circumstance bonus to stealth but a number of simple tactics can easily negate that. Including just walking around doing whatever you like, the gm is well within their rights to assign circumstance bonuses to detection rolls if an invisible mage is blithely walking around in enemy territory.
Others have mention some common anti magic defenses but nobodies mention that a number of effects can be tied to Unhallow including dispel magic/invisibility purge targeted towards any number of triggers determined when cast. eg: "anytime someone who doesn't serve Vlarrbog, God of Unpleasantness enters this area target them with a dispel magic at my caster level."
