Okay so I have done some real world testing to show the impact and isolate the problem area. That's a bit longer post but it needs that to show where the problem is.
Configuration: DS412+ with 3TB WD drives running RAID 5 with one Volume DSM 4.0-2228. Network connection all hardwired 1GB/s ports via Airport Extreme Router and Netgear 5-port Giga Switch. External HD is a WD Studio via FW800. Two Macs, one a Mac Mini running a RAID 1 and one iMac27 with standard 1TB HD.
Two test subjects of data to transfer:
1) Small Set - Folder with 4.84GB of various drivers for hardware (drives, config files, docs, executables, etc.)
2) Big Set - Mountain Lion Install Image with 4.37GB (a few smaller files but basically one large DMG)
Baseline: Transfer both folders from external FW disk to local internal disk
1) Small Set: 1:39min ~ 50 MB/s
2) Big Set: 1:11min ~ 64 MB/s
This is helpful to see that there is a difference in between transferring lot's of small versus large file even locally. This also shows the pure performance difference without any network impact. Big set is roughly 22% faster.
Network Test: Transfer both folders from Mac Mini to the iMac via a shared folder:
1) Small Set: 2:35min ~ 31.9 MB/s
2) Big Set: 1:39min ~ 45 MB/s
This shows as expected a bit slower performance over network accounting for network protocol etc. which is roughly 32%.
SMB to DS: Transfer of both folders from Mac Mini to the DS412+ (Mounted via smb://dsname/Test
1) Small Set: 2:16min ~ 36 MB/s
2) Big Set: 1:19min ~ 56 MB/s
Similar to previous test the DS is even faster than the Mac-to-Mac and difference is 36%.
So far everything is within expectations and I'd say operational parameters. Now let's move on to AFP ...
AFP to DS: Transfer both folders from Mac Minot to DS412+ (Mounted via Finder)
1) Small Set: 5:51min ~ 14 MB/s
2) Big Set: 1:43min ~ 43 MB/s
Now this is where the problem is. A slight performance decrease as seen for the big set is acceptable but for the small set the performance just bottoms out totally. In this example there is a difference of 68%.
Also i have not tested this but from what i have seen the drop is proportional to the size and amount of files you transfer. So if you transfer something like you Library directory with lots's of small configuration files it just bottoms out and grinds to a halt. The "small set" had some reasonable size files in it so i could get through the tests.