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your e-residence card number is on the back of the card and will have a letter at the end most likely an a so 000000a

an e-residence card in not an id card however companies in Malta ONLY will take it in lieu of an id card.

A Malta ID card is for Maltese citizens and contains biometric information and may be used as a travel document within the Schengen area.

A Malta EResidence card is for those other than Maltese citizens. It is a registration document and does not contain biometric information and is not a valid travel document.

Your number will end in an A (for Alien)

I think the other numbers may be for your EGovaccount but without reading the letter I couldn't say for sure.
Also, though they send those numbers you may well find they do not function as I distantly remember having to go through a process to get them by another method. But then, I didn't bother with an EGov account.

Yup, those PIN numbers are for when you want to set up an eGov account.

I highly recommend learning your ID number by heart, you'll be asked for it all the time.

Interesting, I have never been asked for my number and only once been asked to show my card on the bus (60+).
Also, now remember I had to go through a process at the Passport Office here (on Gozo) to get new numbers for EGov as those initially issued were not valid but as I said, I never bothered with an account.

I use my id number daily, in fact it is my phone number as well as I had more chance of remembering my home phone number by using it!