So just what problems does a nom-mod16 res cause?

I assume the title is fairly obvious. I know AVC (and MPEG-4 ASP codecs) are designed for mod16 and that encoding to a non-mod8 resolution will cause a decrease in compression efficiency. Are there any other ill-effects that this can cause?

Non-mod16 res. reduces speed too 

For some avisynth filters and for some codecs this reduces speed because they have to use more generic routines to process the clip. Many of the "fast" routines are optimized for mod8 and/or mod16 resolutions :) It's logical to use mod16 resolutions since macroblocs in h264 can be as big as 16x16 pixels. If you use another resolution, it's up to the implementation to choose wether to truncate the picture, or clone the last column of macroblocs to extend the picture to something at least mod8, etc ... or simply do nothing and produce a misaligned or completely b0rked picture xD

there is no non-mod16 picture possible in avc. whats possible is making the decoder not show parts of the picture (so when encoding with non-mod16 the encoder will add pixels so your picture gets mod16 but the decoder will not show those pixels, altough they are there)

If you mantain it at least in mod8, it will only decrease the compressibility. If you use an non-mod8 resolution, you can have serious quality loss in the edges of the picture, besides the compressibility hit. See:

it doesn't matter when you only have a non mod 16 clip but it's a problem when you have mixed 16:9 and 4:3 content and therefor really black bars. in the former case i see no sense in ensuring mod8 either