Are SFTP up/download speeds something that's in the control of the hosting company? Can they throttle SSH traffic, regardless of the port?
I just signed up with a new hosting company. We'll call them Slow SFTP, Inc. I have another server with Fast SFTP, Inc. Both are in Dallas and both are in different data centers.
I noticed my SSH client (PuTTY) lagging when connecting to Slow SFTP, Inc., so I decided to run some tests from both companies. I ran several tests over several hours. I also changed sshd ports just to make sure traffic wasn't being throttled based on the port. It made no difference.
| Slow SFTP, Inc. | Fast SFTP, Inc.
-----------------------------------------
UP | 744 KB/s | 352 KB/s
DOWN | 150 KB/s | 1,723 KB/s
I find it strange that the download speed from Slow SFTP, Inc. is so much slower than the upload speed.
Note: These are 1:1 comparisons. Identical setups on both servers. No firewalls. Vanilla Debian 7/sshd installs.
Routing can play a big part in speeds. As seen in the comments the datacenter likely had a bad route and swapped it when performance was suffering.
The two companies can very well limit the upstream/downstream transfer speed with packet shapers. And most likely they do, especially if they're hosting companies. You only have a certain amount of upload bandwidth and a certain amount of download bandwidth. Plus, some hosting companies also meter the actual amount of transferred data, and after a certain threshold they "cut" your speed to a lower limit.
And to precisely address the main point in your question, YES, they can throttle traffic to/from your server (or virtual server) regardless of the port, they can set global limits per-machine, per port-group, or even per-service-type if they have a content-inspection capable firewall.