This is something I've never considered before and wanted the opinions of the experts. We use VLANs day in and day out for various network tasks. My modus operandi is that in general, if something supports VLANs, that port is getting trunked because it just makes a ton of sense if there's even the slightest chance you need to do more than one thing on that single link.
As I ponder this, though, I'm wondering whether there's a performance penalty involved with this line of thinking? Is the impact negligible?
Packet switching in the network gear will always process vLAN information if it is supported. So having vLANs or not, makes no difference in switching speed.
If the packet has to be routed by a L3 router, then there may be a penalty incurred. Similarly if the packet has to be forwarded to a router, you'll have even more penalty incurred for that process.
If the packet is sent out tagged, sounds like this is the case for you since you've got all your ports trunked, then you'll get hit with 32-bits of extra 802.1q header (QinQ doubles that).
This all adds up to almost nothing in the grand scheme of modern networking. I do not believe anyone would notice the difference unless they're implementing a HPC or similar, and at that point they'd be better off implementing some sort of ultra-low latency interconnect rather than trying to tune Ethernet.