Can gigabit media converters affect performance?
I have not seen a latency or performance impact, but it is a maintenance issue... many of these devices are not managable so you do not get good visibility to link error statistics or (in some really bad cases) you dont even get link down on both sides.
I dont want to be all negative, but do think carefully about troubleshooting, rack mounting, error conditions and management for the candidates you consider; I would be interested in your experiences if you find a particularly good device.
There is measurable latency (few ns); it's not noticeable unless your running HPCs or something similar.
We had several small single-port (one in, one out) converters that we used for the same reason. It makes your cable management a little sloppy (as far as keeping wiring nice and tidy) which becomes more and more important as you grow and add servers and more cabling.
The failure rate was also pretty bad. We used two different brands (don't remember what they were now), and both brands seemed like they didn't last long before failing and having to be replaced. This is why we eventually (a year or two later) sprang for a decent rackmount switch with built-in fiber ports.