Yes, one skill check can benefit from multiple synergies.
The synergy system simply says:
It’s possible for a character to have two skills that work well together. In general, having 5 or more ranks in one skill gives the character a +2 bonus on skill checks with each of its synergistic skills, as noted in the skill description. In some cases, this bonus applies only to specific uses of the skill in question, and not to all checks.
Note that it says "bonus" and not "synergy bonus". Thus, the base assumption for synergy is that the bonus is untyped.
Further, both Diplomacy and Use Magic Device omit a type when discussing the bonus:
If you have 5 or more ranks in Bluff, Knowledge (nobility and royalty), or Sense Motive, you get a +2 bonus on Diplomacy checks.
and
- If you have 5 or more ranks in Spellcraft, you get a +2 bonus on Use Magic Device checks related to scrolls.
- If you have 5 or more ranks in Decipher Script, you get a +2 bonus on Use Magic Device checks related to scrolls.
Bonus stacking says that:
In most cases, modifiers to a given check or roll stack (combine for a cumulative effect) if they come from different sources and have different types (or no type at all), but do not stack if they have the same type or come from the same source (such as the same spell cast twice in succession).
The synergy bonuses aren't labeled as a "synergy bonus" to the skill anywhere, so the question is whether the two various bonuses "come from different sources".
In the UMD case, this GM thinks it's pretty clear that "5 or more ranks in Spellcraft" and "5 or more ranks in Decipher Script" are different sources of a bonus (in-game: one is "well-trained in the art of magic" and the other is "well-trained in the art of figuring out what that chicken-scratch is trying to say").
In the Diplomacy case, it's a bit more I think it's pretty clear that they don't stack: the +2 comes from "5 or more ranks in Bluff, Knowledge (nobility and royalty), or Sense Motive". It could easily have been written to match UMD and potentially grant a +6 bonus if all of the synergies triggered, but it wasn't. That said, it's worth noting that the 3.5 FAQ disagrees with this interpretation, stating instead that those three sources of +2 bonuses are different sources and the character would get a +6 to diplomacy (the individual skill listings for Bluff, Knowledge, and Senses Motive do seem to support this interpretation, too), though the FAQ should be taken with a grain of salt. I would read the Diplomacy skill as authoritative and the other skills' synergy descriptions as reminders, but the "+6" reading isn't way out in left field or anything.
From a metagame perspective, I think the more restrictive interpretation of diplomacy's synergy is preferred. UMD is a powerful skill, but one that's relatively hard to boost and which requires significant investment. Diplomacy is fantastically powerful (if used ... right?), but it's (IME) easier to boost and its DCs tend to scale much slower than UMD's; getting an extra +2 or +4 from skills that a character who focuses in diplomacy is likely to take anyway feels just a little too potent.