This whole subject interests me immensely, largely because of the implications of how government issued identifiers would work in an SR-like world.
The first thing to realise is what a SIN actually is - especially when combined with a credstick. Imagine a national identity card (pretty much like the UK government are planning) - there's obviously a lot of resistance to the idea and many people who won't want to carry one. One of the "ideas" that the UK Government has had (sometimes I swear somebody up there is a Shadowrun player!) is to require the card for various services - obviously governmental services, but that will be extended to private industry. Banking will likely be one of the first - your credit/debit cards will be subsumed into the ID card. Transport is likely to be another - not only will the passport morph into the ID card (it's the same government agency responsible and the costs are already being loaded into passports), but cards such as Oyster (used for transport services in London - yes, they track your every journey) will be stored on the same card. Even something simple like buying a beer will require the card - proof of age for a start. There are lots of problems with this - not least is the probability of data leakage; ie, how do you stop any service provider from accessing data for other services stored on the same card (the bar again gives a good example - all the bartender REALLY needs is an assertion that the bearer is over the age of 18. Adding medical record access to the same token could open a world of hurt (and don't get me started on the NHS project to centralise all medical records)
This is almost exactly what the SIN/Credstick is in SR, but there are a few important differences. In order to get a "National Identity" you have to go through an interview process and subject yourself to a full biometric test - all ten fingerprints, retinal scans, photo and (at some stage, DNA). When these tests are taken then duplicates will obviously be blocked - preventing someone from having multiple identities. The main difference is that cross pollination has, as yet, not being seriously talked about. Adding in "untrusted" identity providers to the mix creates a weak spot.
The trick in creating and removing identities is that you're bypassing those controls. The system (even on a small scale like the UK) will become massively unwieldy and those cross checks can't be done at any other time - your friendly decker drops in the entries (birth, school records, tax etc), sets the links against them and you're done.
One of the interesting scenarios resulting from the cross-pollination of IDs is that most citizens actually have multiple IDs - a national one (or potentially two for immigrants), plus a corp one. In this case, I assume the IDs are cross referenced so that a single "identity" is derived.
I'd let someone choose at chargen whether they wanted a SIN or not - there are actually advantages of each - an identity is attached to financial records and that can create a tax liability (didn't Shadowbeat have some rules for this?), plus there's a constant data trail...
Not having a SIN results in huge problems for a person - no shopping at all (except black market - that's what Street Index is for), no transport, no rights. Hence, fake SINS get used - which can be almost as good as the real thing, but still carry some of the same problems.
Having multiple IDs is a good thing - as long as they're /generally/ disposable - once it's dirty then drop it and get another. Buy equipment using different ones so it doesn't look like you're kitting out for a war - move income across different IDs to avoid tax, but not arouse suspicion about your 10,000/month living costs!
When you leave fingerprints on a crime scene then there's no way of knowing which SIN that will get traced back to... could be all of them! That's the reason for also keeping at least one lifestyle as cash only (I recall there are rules for this as well - especially around reduced Matrix services).
One final thing is that when you do get captured/arrested, it's in your interests to assert your identity. "I'm Joe Bloggs" - here's my ID and the DNA sample matches WILL be a better scenario than LS (or another corp) discovering that you have 5 different identities by running a check on you

Retinal Dup and fake fingerprints might also play a role here for the truly paranoid