If you keep your fans running as they were designed by the factory, it should be fine.
Any server with horizontal PCIe cards means their components are on the bottom, so when the heat rises it travels directly into the PCIe board and gets somewhat captured (one reason the Supermicro UIO/WIO design spec was a decent improvement over stock PCIe - they put the components on the opposite side).
If you have fans who push airflow directly into the card, there isn't too much stuff in the way, and the fans are on all the time moving a decent CFM, you should be fine.
If you modified the fans to be quieter (e.g. installing resistors between the fans and the headers), are relying on negative pressure (ie. fans pull the air past the PCIe card instead of blowing on it), or have replaced the fans altogether for some quieter fans that are out of spec, all bets are off.
I'll give you an example: someone sold me an M35 hard drive enclosure on ebay and neglected to put in their listing that they had replaced the original fan with a Gelid low-RPM case fan (like, sub 2000 RPM). I tried it for a while, but during the summer my hard drives would go over 40 degrees C, and would trigger a really annoying alarm. I'm thankful they kept my hard drives from burning up, but it was clear the enclosure had an inadequate fan and it had to be replaced.
Upon researching the original fan spec, I noticed they have high static pressure ratings in addition to being 4500-6000 RPM, presumably because most Supermicro cases pull the air through the hard drives to cool them rather than blowing air over them.
So all the specs could be important depending on how your fans are situated and how they're expected to keep the entire rig cool, but as a rule generally any fan in a server under 4000 RPM will probably be inadequate. The only place you can make an exception is the CPU since its fan is only expected to cool one thing, and it's placed directly next to it.
There are some PCIe slot blower fans you can find if you have an empty 2nd slot, I've got one in a rig cooling a SATA drive that's in a PCIe slot holder because the old ones get pretty hot under load and that particular rig has only 1 120mm 1200 RPM fan for the entire case. So the blower fan pulls the air through the front of the case (where there's 4 x 2TB hard drives) right past the SATA drive in the PCIe slot next to it, and blows it out the back.
I'd rather have a second 120mm blowing directly on the 4 HDDs, but you get the idea - you can make things work. Here's an example:
StarTech.com Expansion Slot Rear Exhaust Cooling Fan with LP4 Connector FANCASE (Black) - Newegg.com