The notion of a referendum being "illegal" is farcical. No democracy should prohibit people from deciding to get together and conduct a poll on something.
The idea of a referendum being "illegal" may be counter-intuitive, but I don't think the situation is as simple as you suggest.
For example, secession (not to mention sedition or treason) is illegal in many jurisdictions, and is a natural thing for sovereign countries to want to prevent. It is also natural for the sovereign central government of a country to put limits on what a regional government can and cannot do, with the usual principle being that the regional government cannot do anything outside of the powers specifically given it by the central government (regardless of what powers the inhabitants of that region want).
You're right that "people" could "get together and conduct a poll on something", but if this was informally conducted it would be hard to prevent double voting, and not accidentally disenfranchising certain people, and there would be little recourse against these self-appointed pollsters stuffing their home-made ballot boxes.
At the same time, if a regional government spent money, or used people's personal information, for a purpose they were not legally permitted to, then those would potentially be crimes themselves, regardless of the issue of secession.
The questions worth debating are "How much autonomy should regions of sovereign countries be given?", and "If a region isn't legally given that much autonomy, what is most peaceful and just means for that region to attain it?"
Secession can certainly be illegal, but that simply means any outcome of an unsanctioned referendum is legally irrelevant.
As far as I can tell, Spain is going to great lengths to curtail the rights of citizens to express their opinions on secession. They're free to ignore the outcome of this vote, but raiding ISPs, shutting down political pamphlets, and reading private mail are not the actions of a democratic country—they're tactics straight out of an authoritarian regime.
Secession is also illegal in the US (and we fought a war to prove it), but you don't see federal agents arresting people for starting ballot initiatives in California or shutting down Vermont secession websites.
Neither do you see the government of California or Vermont organising a binding vote to secede from the US in 48 hours (while maintaining the US citizenship!).
