Spell Slots: The various character class tables show how many spells of each level a character can cast per day. These openings for daily spells are called spell slots. A spellcaster always has the option to fill a higher-level spell slot with a lower-level spell. A spellcaster who lacks a high enough ability score to cast spells that would otherwise be his due still gets the slots but must fill them with spells of lower levels.
Bolding for emphasis.
They can also use those slots for metamagic of lower level spells. Except for heighten spell, metamagic does not actually increase spell level, so it's possible to use those higher level slots for metamagic even if you couldn't cast spells of that level.
I do not think this is true. The general rule for metamagic feats is that the caster uses the original level or the modified level, whichever is more disadvantageous. That's why a maximized fireball cannot be put in a wand (this limitation is a disadvantage), but is saved against as a third level spell (because it's easier for opponents to avoid). Similarly, it requires a more difficult concentration check than an unmodified spell, but would be treated as a third level spell for being dispelled.
The inability to cast spells is certainly a disadvantage, and so it would apply.