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I (also) use external hard drives for backup. For full backups I attach them directly via USB to a Mac, but most of the time they are attached (still USB)to a Linux (Raspberry Pi) server, where I can access the files or use rsync for incremental backups.

That means I need fast, native access from Mac, and relatively fast access from Linux.

Once in 2-3 years I have to access things from Windows, and Samba is definitely good enough for that.

I've also noticed speed issues with the fuse-supported NTFS on Linux.

Was that just my perception?

and are there substantal counter-arguments to using HFS+ in these circumstances?

or would I be better off with NTFS?

HFS+ support on Linux is mediocre at best. In theory, it's supported, but filesystem checking is essentially nonexistent without a lot of manual work, and it has issues sometimes if the filesystem was not cleanly shut down. Performance is also not particularly great, and the driver is not widely used with means it's more likely to have undiscovered bugs. I'm not sure how well it's supported on Windows as I've never dealt with it there.

Given all of this, I'd say that it's probably not a great choice unless you can 100% guarantee that the hardware will never have issues that cause the filesystem to have errors.

NTFS has it's own issues for this type of thing. On Linux, you essentially need FUSE for it, and it's not natively supported by macOS. I've not tried it on macOS, but the Linux FUSE module isn't horrible if you're dealing with a fast storage device (I use it without significant performance problems on an SSD, though I would be hesitant to use it on rotational media or a flash drive). Given that Windows support is not a high priority for you, I would look elsewhere.

This leaves a handful of other options, many of which are at best mediocre:

• FAT32: Natively supported on both macOS and Linux, performance is decent as long as you're just doing writes of whole files at once and not doing in-place file updates, and it's trivially usable from Windows too. The big downside here is that it has a really low limit on file size compared to most other filesystems. Most well designed backup software can handle this fact without issue though (because it will archive everything to a single file, and can then split that across multiple smaller files to stay under the file size limit), or you can bump up the cluster size when creating the filesystem to increase the max file size at the expense of higher potential for wasted space. It also doesn't preserve most UNIX attributes, though you can work around this by using archive files instead of flat file copies.


• UDF: This is the filesystem format used on DVD's. It also happens to have support for more conventional block storage devices like hard disks, and it's natively supported on both Linux and macOS. Performance is decent but not amazing. Just like FAT32, it doesn't preserve most UNIX attributes, and you can work around this in the same way. There's also an issue in that the Linux driver is a bit buggy, and Linux has almost no filesystem recovery options for UDF.


• UFS: Limited native support on both macOS and Linux, both with decent performance for typical backup workloads. Tools for working with it form userspace are somewhat limited in both cases, and it's somewhat expected that support may be going away on macOS in the near future (if it hasn't already been removed in the most recent macOS version).


• ext2: Native support and great performance on Linux, needs special drivers on macOS but gets decent performance. This is probably your best bet if you're usually using the disk from Linux, as it gets you proper filesystem recovery support on the system you will use it on most of the time.

HFS+ is the Apple's filesystem, meaning that it can also be accessed by third party software (considering other OSes as software in general, here), but it doesn't have to be, it's up to the other OS support for it.

Having worked for many many years with Windows and still doing it right now I can only confirm that is one of the most not-supporting-anything-but-MS-software type of ecosystem nowadays, such as Apple was until they finally accepted the USB-C as a standard in the new laptops and iPad...

NTFS by the opposite, yes was produced firstly by Microsoft (not sure if it's still a proprietary software or if Microsoft is still working on it) but at least I never heard of any single operating system that does not support reading and/or writing files on NTFS (except Android until the latest versions which I think that finally have that support).

I would personally stick to NTFS because of compatibility, and working on a Linux and MacOS environment (and Windows only occasionally, from what I've understood by the tile), means that you can also take advantage of the case sensitiveness supported by this FS.


EDIT:
As pointed out by @tetsujin in the comments, NTFS is not actually compatible with MacOS natively so my final suggestion would be to actually stick with something even more known and universal as FAT filesystems (ExFAT to be precise because is the Extended version and supports files larger than 4GB, at least).