Vertices & edges vs. nodes & links
And what if the next author likes neither your terminology nor the previous one and decides to call these elements bars and joints? And then the next one goes for arms and knees?

I'm an electronic engineer: what if I decide that I don't like the terms resistance, capacitance and inductance, and I decide to use the terms opposance, tankance and springance? 

Readers should not struggle to follow author's idiosyncrasies about terminology, the effort is already enough to understand the new concepts that are typically introduced in a paper. And recall that the first readers of your papers are the reviewers, and sometimes the reviewers complain for even more conventional terminologies. Moreover, if you are free to make your terminology choices, they have even more freedom in rejecting your paper.

Here is an example. As I said in the above, I'm an electronic engineer. However, due to the tradition of the field in which I work, most of my readers are physicists. When I write a paper, I typically use terms and symbols that are widely employed by the engineering community, and are even defined by standards. For at least three papers, the reviewers complained that I haven't used standard symbols or terms (standard for them). And so I had to reply with references to standards, literature etc. It's annoying, but at least I had references to provide, and eventually symbols and terms were accepted. What do you have to backup your choice of terminology?


  I think it's more intuitive (to a modern audience) and it would be better if people adopted this convention


Aren't you generalizing too much?


  we'll never get rid of all the poor choices made in the past.


Are you sure that there are so many poor choices?


  So my question is, is it acceptable to use nodes/links?


I think not or, better, as I explained above, I think there is no sound reason to use nodes and links in place of the accepted terminology.


  Is it ever smart go against convention, just because you don't like how things are done?


It is seldom smart, unless there are good scientific reasons or the existing terminology is really misleading, but before going against an established convention, you have to provide evidence that that convention is wrong or misleading. An example in this sense is that of relativistic mass, a term which was introduced at the beginning of the theory of relativity. In later years, however, the concept has been criticized [see e.g. Adler(1986)] and the term is now considered utterly misleading, and modern books on relativity avoid it altogether.