SBS2011 to Exchange Online

Just like you can have more accepted domains in your local Exchange Server, you can have multiple domains under the same Office365/Exchange Online account.
AD Sync is a whole other case though. The official tools don't seem to be fully supported (ex. DirSync).
If you find you can manage the users manually, this is a good route to go. If you REALLY can't manage all the users (because to great an amount of users), you'll have to get a newer DC server (2012R2 or newer, but obviously, that also means a full domain migration).

Exchange deployment assistant
https://assistants.microsoft.com/

Mail migration assistant:
https://aka.ms/MailSetupAdvisorFromEDA

Exchange Online (ExO) can manage any number of domains that you want.
you just need to add them into the "domains pane" on the O365 admin panel

The procedure can be implementing a hybrid deployment with AD and AAD
or can be just done using a cutover migration if there are few people (less than 300).

The users are currently 25-30 so they are not that many  so as to not be able to administer them in two places. How will the exchange be removed from SBS2011 though?

I thought that it is deeply ingrained and cannot be removed without breaking the whole thing.

You can just disable it. You don't fully remove it. You just leave it dormant. Just make sure all the necessary Exchange Online data in the DNS are pointing outwards (most important are the autodiscover and following data inside it). This is only necessary if your local domain is exactly the same as the domain name of your mail.

For 30 users you can do cutover migration. Refer:
https://docs.microsoft.com/en-us/exchange/mailbox-migration/cutover-migration-to-office-365

That depends. If there is a plan to go further down the O365 and Azure Active Directory integration route then it's a good idea to properly remove Exchange and look to setting up a new server with Hyper-V and a DC guest and a file and print VM guest that can also run any needed business app back ends.

If they are heavy Microsoft Office users then look to the "E" series plans with Microsoft Office and SharePoint Online integrated. Then, the need for a local server can possibly be met by a full-on O365 setup.

If its standard by-the-SBS-book wizard stuff youve been doing on the SBS server the guides above should be good.
if you've ever tweaked any settings outside of SBS wizards you may find some of the guides don't quite match  the steps you'll end up taking.
(SBS is an odd beast and hates being customized)

If this SBS is critical to the business, take serious care. Peoples jobs may be on the line here so get good backups of everything at every stage and consider getting someone in who has done it before (as SBS migrations tend to either be straightforward or a bit of a nightmare).

As to disabling/removing Exchnage afterwards, that is customization and SBS hates it. Removing it is a bad idea but disabling it can work. As it is customization you may find that some of the SBS updates/wizards are affected in the future, but it does work in the most part.

Only big warning from me is if you happen to use the same 'AD' domain as any of your external e-mail domains. This can cause some confusion with DNS entries but can be resolved as long as you know about it in advance.

I will probably go through with it but will ignore any integration with the SBS/AD. Since they are a small company 20+ people, I will recreate all users on the Online part and start moving the emails  the old fashioned way (Export to pst->Import).

Am I correct to assume that once the mx/a/dns/autodiscover are setup for the online, it will ignore the SBS2011 setup?

Office365/Exchange Online, by default are set up online, and will indeed ignore SBS2011 setup (as nothing of this setup is known to the MS online server).
However, if there are conflicting DNS entries (online, vs local SBS2011), you'll have to adjust it in the SBS environment to match the online entries. Otherwise Outlook will look for local servers instead of the online servers (in case of local domain matching exactly with the FQDN online)

Am I correct to assume that once the mx/a/dns/autodiscover are setup for the online, it will ignore the SBS2011 setup?

Effectively yes. The issue you'll have is that the user's local AD accounts will still be associated with the local exchange install, even though you arent using it.
Recommend creating new outlook profiles for the new O365 users to keep remnants of of the old accounts to a minimum.

When cut-off day arrives, this step needs to be run on the Exchange server/DC:

# Check SCP:
Get-ClientAccessServer | fl name,AutoDiscoverServiceInternalUri

# Set SCP:
Get-ClientAccessServer | Set-ClientAccessServer -AutoDiscoverServiceInternalUri https://AUTODISCOVER.Domain.Com/autodiscover/autodiscover.xml

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Set to the O365 AutoDiscover setting to make sure all internal clients do not attempt to connect to the on-premises Exchange after cut-over.

Sorry for the late reply. I've been trying to convince them to go through with it and finally succeed. I'll start with company3.com which is only 3 people. The only issue I can think of, is the fact that one of them is part of a Distribution group on the SBS and they are also using Room Resources from the SBS.

How can I replicate this using Exchange Online? Or when they are booking a room, they just need to send an email to the room and it will work?

Exchange Online has the same abilities, and more, as the on-premises Exchange.

Set up the room resource mailbox, set permission levels, and auto-response levels, and go.

Yes but as these three users will be online and the rest on-premises, how will the room show as booked if the online user books it. I've been reading about hybrid but I see that SBS doesn't support it.

Once they are migrated into O365 the on-premises Exchange in SBS gets uninstalled. Before Exchange being uninstalled check the Service Connection Point making sure it is pointing to the correct O365 Autodiscover URL.

Once Exchange is gone on-premises this becomes a moot point.

Yes but the transition will be in stages. First the three users of company3, then the other 10-15 of company2, then the last 5 of company1.

Until this finished, is there a way to allow the company3 users to have access to rooms and distribution groups currently setup on SBS?

not really, no. they'll be separate e-mail systems unless you go fora hybrid setup/transition (which can be really tricky with SBS.)