I think this question is a bit old but I had a similar problem and solve it using the info in this post: rCharts nvd3 library force ticks
Here my solution for a base10 log-scaled stacked area chart, it shouldn't be too different for a scatter plot.
df<-data.frame(x=rep(10^seq(0,5,length.out=24),each=4),
y=round(runif(4*24,1,50)),
var=rep(LETTERS[1:4], 4))
df$x<-log(df$x,10)
p <- nPlot(y ~ x, group = 'var', data = df,
type = 'stackedAreaChart', id = 'chart')
p$xAxis(tickFormat = "#!function (x) {
tickformat = [1,10,100,1000,10000,'100k'];
return tickformat[x];}!#")
p