A 16-bit CD-ROM driver loaded in real-mode e.g. will cause Windows to access the CD-ROM in 16-bit mode. At least Windows 95 does that. It's even displayed somewhere in Winows if that happens; can't tell by heart where exactly, thought.
I did a quick test of how Windows 98 SE sees devices with DOS drivers loaded (CTMOUSE, VIDECDD, SMARTDRV, EMM386 and DOSKEY). Indeed System Information shows these drivers being loaded (under MS-DOS drivers), but there is no indication they are being used. In the Device Manager, the mouse shows as 'PS/2 Compatible Mouse Port' using VMOUSE.VXD, MSMOUSE.VXD and MOUSE.DRV, the CDROM drives use MSCDROM.INF, hard drive uses DISKDRV.INF.
Furthermore, all drives show as operating in DMA mode. The System Properties --> Performance tab says "Your system is configured for optimal performance". There is no "Drive X is using an MS-DOS compatibility mode file system" message.
The only thing different if I skip loading all DOS drivers, is that they do not appear in the System Information summary, but everything else is the same.
1. This is Win98 SE; older versions may be different, e.g., Win95 as you say.
2. I did not benchmark actual performance
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