A short answer, but the player's might consider contracting with the top level crime syndicate itself. Instead of investing tens of thousands of gp around defenses that may or may not work while they are away, they could, in effect, pay a smaller 'protection tax' over time direct to the organization they are worried about. Word (should) also get out to lower level guilds or miscellaneous rogues that their place is under protection and it will be (mostly) left alone, at least from the real heavy-hitters. Cost of doing business...
For extremely valuable items, if the party is away for awhile, Leomund's Secret Chest might be ideal if they have access to the spell. Spells like Glyphs of Warding, Fire Traps, Sepia Snake Sigil, maybe even Mordenkainen's Faithful Hound could also be useful.
I don't think you are going to be able to stop a determined attacker with anything short of a hired army while you are away, so the important things will be to
- Try to negotiate to prevent a determined attack from happening
- Make sure if it does, the best items are unavailable
- Buffer with some guards and other magic wards to dissuade anyone less determined.*
*Since you don't want anything harmful going off on 'some kid who has wandered into the basement', you probably want these kinds of devices to be of a non-lethal variety or behind a locked door or guard that would block a wanderer.