It depends on the SATA version, the PCI slots and on the drives.
Lets start with PCI, which comes in several flavours:
- 32 bit, 33Mhz.
- 32 bit, 66Mhz.
- 64 bit, 33Mhz.
- 64 bit, 66Mhz.
The first option (a 32 bit wide PCI bus running at 33MHz and at 3.3v or 5 volt) is the most common. You will find it in most older computers. (In more modern computers you will find PCIe instead).
The 32b/33Mhz configuration is theoretically capable of transferring up to 132MB/second over the PCI bus. (4 bytes per transfer, 33M transfers per second).
You can determine which PCI version you have by looking at the diagram below.
(Image courtersy of wikipedia's article on PCI).
Next up is SATA.
- SATA-1, aka SATA 1.5Gb/s is capable of transferring up to 1½ Gbit/sec.
- SATA-2, aka SATA 3.0Gb/s is capable of transferring up to 3 Gbit/sec.
- SATA-3, aka SATA 6.0Gb/s is capable of transferring up to 6 Gbit/sec.
These are also theoretical maximum values in bits.
In practice a good speed for SATA-2 is about 270MB/sec.
That is almost twice as fast as the most common PCI bus.
Which means that the answer could be: Yes, the PCI bus will be limiting the speed.
Could, because I ignored two more points:
First of all the drives.
If you have a harddrive which can not fill the PCI bus then it does not matter that SATA-1/2/3 is faster than PCI (32/33). Neither will max out.
This is the most likely scenario when using older drives. (Current top speed of mechanical harddrives is about 200MB/sec for 15K RPM enterprise level SAS drives, and about 100MB/sec for modern consumer 7200 RPM SATA drives).
Secondly PCI is a bus. The bandwidth is shared by all devices on the same PCI bus. If your other on-board SATA controllers are on the same PCI bus then they will compete for bandwidth.