I'd probably say no to both bonuses and penalties. The zombie, for sure, has changed creature types from humanoid (human) to undead. It has lasted for centuries in your example, and has no maximum 'life' span, so obviously physical penalties make no sense. Being unintelligent, it has nothing "upstairs" to begin with, let alone improve upon.
The vampire is a humanoid (human) with a template that alters the creature type to undead. A case could be made it still gets the mental bonuses (this fits with many cases in fiction), but the penalties go with them automatically. And how do you penalize the vampire's non-existent Con score?
Based on rules, nothing to go on. I'd personally go with no physical penalties for both, mental bonuses to the vampire. While many undead are shown as being somewhat 'set in their ways', never changing or growing, adding those bonuses gives a way to bump up the power of a vampire without just tacking on more templates or class levels.
I'd say, by the example undead NPCs we've seen in Pathfinder adventures, that undead do not gain ability score bonuses for aging, for the same reason that elves gain ability score bonuses for age at a slower rate than humans. For whatever reason, the game's rules assume that older creatures are biologically smarter and wiser than the young. Undead, even free-will undead, have cut themselves off from this natural development, so they do not gain these bonuses normally.
Of course, it doesn't make sense from a realistic perspective (the older are generally wiser not because of biology, but experience, which is represented in levels).`But most intelligent undead have enough bonuses without being tempted to give them extra already.
Well to start with; the entry for a human and the entry for a zombie (even one from a human stock) are completely separate entries.
Undead creatures (usually) don't even have the Humanoid (Human) type, instead having the Undead (Augmented) type.
Logical conclusion: you don't apply a rules subset (aging modifiers) that only effect one specific creature type to another, different creature type. You also don't apply the dwarf aging chart for a human, as a bad example.
Another way to look at this is what does the aging chart represent?
It represents the different stages between categories. ←←You are born.. Start adventuring.. Grow old.. Die and become dead (or undead)→→
The chart represents the time between the start of your adventuring career and when you die of old age (or earlier). Mechanically you change into either an object or an undead at this point.
Third way to look at this; aging bonuses/penalties make no sense for an undead. A zombie also doesn't have a max limit where when he gets a certain age he dies. Again. His body doesn't grow old and frail with age. In fact most zombies in ancient tombs are themselves ancient.
The bonuses are nice, but 2 out of 3 parts of the chart don't apply, and the third is really awkward when you try to shoehorn the age categories into fitting.
you don't apply the Humans Only rules to non-humans such as zombies or undead.
Now, the real question is what do you do when an already venerable human then becomes a zombie/vampire/undead?
Another argument against this is the Aging Effects Chart, listed as Aging Effects.
Then in different spells and such they are listed as being immune to Aging Effects, or the Effects of Aging.
Scepter of Ages;
"...Constructs, outsiders, and undead are immune to the effects of aging..."