I make daily backups to TimeMachine, as recommended. In case my Mac breaks down or after formatting this would allow me to restore the Mac to exactly its state, however I wonder what would happen with Devonthink. Would its file structure be maintained? Would tags and deeplinks (and also for indexed items) be maintained?
DT doesn’t do anything other apps don’t do.
Hence: Either you trust TimeMachine with all your data, or you don’t and revert to another backup solution that seems more trustworthy to you. I can’t imagine any backup product to exclusively backup DT files incorrectly.
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So internal relations and metadata will also be maintained? I am especially interested in deeplinks of (non-internal) indexed items, I use them extensively and would not like to have to relink them all.
With due respect, @chrillek already answered the question. 
Anyway, I urge you to do your own testing. Take restore database from TimeMachine (can go into new copies) and see if the restored versions meet your expectations with respect to DEVONthink database integrity and all the indexed files your databases “point to” in indexes. Good if you reported back here your success.
It’s also a good idea not to depend only on Time Machine but also to have e.g. cloud backups or complete, archived backups on external discs.
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A proper backup shouldn’t modify the data being backed up. Restoring data should bring it back in the same state it was backed up. If it doesn’t, you’re either using the wrong backup strategy or potentially have a hardware issue. That would be well beyond our scope to address.
And as mentioned, having secondary or tertiary backups, including an off-site backup, is suggested for data you can’t afford to lose.
This is a very good idea. I noticed that on your site in addition to Time Machine you suggest Arq for a similar option. Is this still the standard for DevonThink users, or do you propose other fine choices in the meantime?
Lots of people here use Arq, me included.
Not because anyone from DevonThink recommended it but it got good reviews amongst the users in this forum.
Also recommended- Carbon Copy Cloner (or similar). Makes a full clone of your drive, not a snapshot backup like Time Machine. Lots of people here use all three methods, if not exactly those apps.
What does that give you?
Arq = off site snap shot back up, versions and history if you have the right level of service.
Time Machine = local snap shot back up, versions and history. Can get you that file you deleted by mistake. Or that corrupt database (heavens forfend!) from before the corruption.
Carbon Copy Cloner = complete clone of your system drive. Can get you back to where you were when a hard drive dies. Gets you back to the state at the last clone operation.
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I thank you for your very on-the-spot reply. I’m looking into Arq and it seems like the best case scenario (do you use the included 2TB plan)? The only thing that worries me is that as I don’t have a very fast connection, and a not state of the art Mac, it impacts my connection a lot by slowing it down through constant file uploads (as well as impacting cpu).
Our company president, @eboehnisch, has long used Arq 
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You can throttle uploads and also be selective about what you back up. Also, you can run backups at night.
I use Arq Premium which includes 1TB cloud storage
I also have it backup the same data to an external drive
Complete restore from TimeMachine?
TimeMachine has always worked well for me,
and did a full restore on a new Mac
(Note: I have no indexed files)
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Forgive me for the possibly stupid question, but this is the first time I would use such a service. Does the upload take place at night even if the computer is locked and idle?
This in itself is a more than excellent endorsement! You speak in the past though, did he switch to another service?
No, still using it 
It can also wake up your Mac and upload at night, yes. I’ve set it to start uploading at 6 p.m. when I am (usually) done with the day’s work.
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What happens with a database that is connected to CloudKit when I restore an old Backup from Time Machine? Will I get the restored state on every synced device or will the old database be updated with newer data from the Cloud?
It’s highly recommended to either restore a backup & clean the sync store or to import the latest copy from the sync store.
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Slightly off topic, but a quick question about Arq. I use Synology Drive as a back up photos, which works but the problem is that each 1TB of data seems to require 2TB of storage, which fills up my HDD very quickly. I appreciate that versioning takes space, but I do not see why a file that never gets changed (a camera’s RAW file) should need this much space. It makes me wonder whether switching from Synology Drive to Arq might be an alternative to buying larger HDDs for the Synology DS.
It makes me wonder whether switching from Synology Drive to Arq might be an alternative to buying larger HDDs for the Synology DS.
This feels very much like apples and oranges to me.
One is a local storage; the other is online. So it’s not an even exchange.
In my mind, there is not only a process difference, but a philosophical one, i.e., one stores your data on your devices, the other stores your data on someone else’s servers.
Thank you. My mistake. I had assumed that Arq would store the data anywhere you told it to and wondered whether it might use disk space more efficiently.