Yes, that might be a good idea. Personally, I have never noticed problems with the new Avisynth+, and all 32-bit plugins I use are compatible (at least all plugins used by BD3D2MK3D). But I cannot be sure that a problem cannot occur with other plugins.
Also, note that it is possible to install only the 64-bit version of Avisynth+ (just untick the 32-bit version in the GUI of the official installer), and your original installation of Avisynth 2.6 will not be modified. BD3D2MK3D uses preferably Avisynth+ 64-bit when it is available, and old 32-bit only programs will continue to use the classic Avisynth 32-bit.
(If you have installed both versions of Avisynth+ with its official installer, and you kept the option to keep the old "classic" files and plugins, you can just uninstall + to restore the classic version, and then install + again, but this time, be sure to untick the 32-bit option. Not sure if that works with Groucho's installer.)
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