It will not slow the access speeds. The 7200/5400 rpm refers to the spindle speed of the drive only. 5400 rpm drives will have slower seek times and increased latency, but the drives do not affect each other, unless both drives are on the same channel. In which case, the drives will sequentially share the channel and experience delays while the other drive is being accessed. In the event that the drives have differing ATA modes, the modes will run as the fastest available mode during access if the motherboard has dual fifo buffers(all current boards and many older boards). If a drive is in PIO mode, the channel will revert to PIO mode only and slow the channel.
Even if not transferring between drives, the 5400 will have a slower data transfer rate due to the spindle speed. If the OS is loaded on the 7200 drive, it will also be contending for the channel with the OS and will increase latency. A better solution would be to locate the drive on another IDE channel or a PCI IDE controller. The extra cost for a 7200 rpm drive is minimal and would be worthwhile if you do not already have the drive.
It's impossible for a 7200RPM drive to slow down to 5400RPM without completely FUBARing the drive in every way humanly possible. It doesn't matter if you used a 300YD IDE cable with power electromagnets wrapped around it, the 7200 RPM IDE drive would still continue to spin at 7200 RPM, although you'd get *0* bytes of throughput.
Remember to try to keep the drive with the OS and everything else that is accessed often on its own channel. Storage drives, burners, ZIPs, etc. Should go on the secondary channel or a PCI card IDE add-on controller. Unless you're in an extreme situation (like me), don't put burners on the same channel with the HDD you're burning from.