If I download morrowind from steam, rather than disk, will it affect any modding?

No.
Except that you will have to redate the Morrowind BSAs back to their original dates.
The MW Code Patch will do that for you, so it's not a problem.

Since you're new to modding, the http://www.gamesas.com/index.php?/topic/1060141-mod-recommendations-for-new-players/page__hl__recommendations has all the info you need on how find/install/use mods.
And which tools/patches you'll need.