Still, it is generally preferable to connect older drives and CD-ROMs to the secondary channel. If this is not feasible, or if you're wondering if you should upgrade, a few points. The speed loss usually referred to is in the interface timing, i.e. the speed at which the devices communicate with the computer. This does not necessarily translate into a real world performance penalty. If you have an ordinary ISA IDE interface, it can't get any slower.
Some interfaces support distinct timing for master and slave.
With these, the slow device does not affect the fast one. PIO mode 3. This is more than enough to operate any harddisk on the market today at its maximum speed. As long as one unit on a given channel is executing a command, the other is inaccessible. A CD-ROM can easily occupy the channel for 300ms that way.