Its rarely straightforward - as it will depend on your system components. For example, some video cards have drivers with completely different performance in 98/2k/XP - even for quite basic functions (i.e. 2D) that mame uses. Gaming cards can sometimes have lacklustre 2k drivers as driver developers assume it is less important.
It can be more complicated though - win98 allows programs much more direct access to hardware (which is faster) than 2k/xp which keep tighter reigns on programs to reduce crashes. This extra layer can sometimes rely on drivers by the likes of SIS, INTEL, ALI or VIA depending on the chipset on a motherboard and performance can vary. Some chipsets had horrendous performance under a different OS (eg early VIA drivers) - and even if updated drivers improve things people often miss getting them as they are not graphics drivers and they don't realise to look for them.
Also, 2k/xp are definately more resource (memory/cpu) hungry than 98 - so for example someone with 64mb or 128mb of ram may find that performance in 98 is great, but crippled when using 2k on the same pc. However - if they had 512mb, they may find performance extremely similar between 2k/98 - and thus choose 2k for stability.
To get back to the original post question - if you are worried about this simply because of mame performance, don't be. Otherwise its a size of HD/other features type of question.
(Apologies for some glaring technical simplifications to try and get a point across!

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