Those with uncanny dodge, simply can't lose their Dex to Armor Class, this does not mean that they are not surprised/flat-footed.
When flat-footed, like everybody else, they can't take immediate actions for example. Also invisible creatures still have the +2 to attack against them.
For all reasons and purposes they are treated as flat-footed/"surprised".
Now as far as the benefits go... apart from the obvious (retaining Dex) they cannot be sneaked attacked. This is because SA demands that one is deprived of his Dex bonus, not that he is "flat-footed".
Uncanny Dodge (Ex)
Starting at 4th level, a rogue can react to danger before her senses would normally allow her to do so. She retains her Dexterity bonus to AC (if any) even if she is caught flat-footed or struck by an invisible attacker. However, she still loses her Dexterity bonus to AC if immobilized.
If a rogue already has uncanny dodge from a different class she automatically gains improved uncanny dodge instead.
EDIT: It's probable that by "can't be
truly surprised", you meant the above. Still I just wanted to make it clear