[RPG] Does Alter Self remove a creature’s existing abilities

From reading the spell it looks like you don't get tremorsense so you're perception would be limited.

There's nothing to stop you from making perceptions checks though with some limitations. Vision is going to be largely useless except for what's directly in front of you. So with the appropriate knowledge you can determine what kind of rock/dirt/material you're in but other then that you can't determine much. Effectively you're blind with an exception of "I can see whatever my eyes are physically in contact with".

Hearing still works but I'd apply the modifiers for listening through a wall (along standard distance modifiers).

If someone is walking around in a room above/below you could also apply the DC to detect a creature burrowing beneath you.

So in summary, you're only as blind as your perception score makes you!

Stat Changes

It seems very clear that you apply no stat changes.

This ability functions as a polymorph spell, the type of which is listed in the creature's description, but the creature does not adjust its ability scores (although it gains any other abilities of the creature it mimics).

There are no qualifiers here -- it says the creature does not adjust its ability scores, so it doesn't! The part of polymorph that you're looking at says that you

adjust its ability scores to one of these two sizes using the following table

This is exactly what the change self ability tells you to ignore.

Even though it doesn't use the word "adjustment" in the actual text of alter self, the word would generally mean any change to your stats. (And it would be a bit weird if shifting into a smaller form increased the strength of a Titan.)

Other abilities

There's nothing here to modify how polymorph spells work:

While under the effects of a polymorph spell, you lose all extraordinary and supernatural abilities that depend on your original form

Note the qualifier. You only lose the ability if it was contingent on your original form. In many places the DM will have to make a judgement call on whether that applies. But obviously, say, a manticore that shifts into human form can no longer use its Spikes special ability. The rule is intended to rule out nonsensical situations, so the change shape ability doesn't alter these rules at all.