No, not for dispelling spells. Mage's Disjunction automatically works vs. all spells and SLAs.
That is, spells and spell-like effects are unraveled and destroyed completely (ending the effect as a dispel magic spell does)
Magic items do get a saving throw. If they are attended items, they use the bearer's Will save.
and each permanent magic item must make a successful Will save or be turned into a normal item for the duration of this spell. An item in a creature’s possession uses its own Will save bonus or its possessor’s Will save bonus, whichever is higher. If an item’s saving throw results in a natural 1 on the die, the item is destroyed instead of being suppressed.
Basically, if the party gets hit by a Mage's Disjunction the game is going to take a pause for an hour or so while everyone recalculates their character's stats.
Here's one. It has an area and duration. Does this create a bubble such that magic items entering the area are disjoined as well, or is the area only relevant at the time the spell is cast, the duration only applying to items in the area at that time?
Works pretty much like an anti-magic field. Level 9 spells... whatchagonnado. Hope you can make your (items') saves.
To answer the OP question: No. You just start rolling saving throws for all the items in the field (or that come into it while it is up).