Bootstrap size and probability of drawing distinct observations Suppose we draw a sample of $k$ out of $n$ numbered balls without replacement and get a sample of $N_1$ (unique) balls. We then replace all the balls in the urn and repeat the drawing a second time to get again $N_2$ (unique) balls. 
We are interested in the set of balls that end up being drawn exactly once (over the course of the two experiments).
It's clear that the probability, for one of the balls, of the event "being drawn exactly once" is
$$2k/n(1-k/n)$$  
which is maximized at $k^*=n/2$. 
Now consider the same experiment but with replacement and we look again for the value of $k$ (denoted now $\bar{k}^*$) that maximizes the frequency of the event "being drawn exactly once". Now, the expected number of distinct balls in each draw is $1-e^{-1}\approx0.632n$ and so I would have expected $\bar{k}^*=k^*/(1-e^{-1})\approx0.79n$. Running some simulations I get that the actual location of $\bar{k}^*$ seems to be much lower, probably between $0.65n$ and $0.7n$. I have a hard time understanding where is my mistake.
More generally (second question) I'm wondering what is the distribution function of the proportion of balls that are drawn exactly once in the second experiment (the one with replacements) as a function of $k$? Through numerical experimentations, I get the following curve ($n=100$):

EDIT
here is the R code to reproduce the example above:
fx02<-function(ll,n,k){
    a1<-matrix(0,n,2)
    a1[sample(1:n,k,replace=TRUE),1]<-1
    a1[sample(1:n,k,replace=TRUE),2]<-1
    sum(rowSums(a1)==1)/n
}

ss<-(1:60)*5   #The grid of values of k for which we'll compute the probability.
a4<-matrix(NA,length(ss),2)
for(i in 1:length(ss)){
    a2<-ss[i]
    a3<-c(lapply(1:1000,fx02,n=100,k=a2),recursive=TRUE);
    a4[i,]<-c(a2,mean(a3))
}
plot(a4,xlab="k",ylab="frequency of distinct draw")

 A: EDIT after seeing your code for the simulation
I think you did not consider the fact that a certain number can also occurr more than once within one sample. After accounting for that, we get the same results. Here is your modified code:
fx02<-function(ll,n,k){
  a1<-matrix(0,n,2)
  samp1 <- sample(1:n, k, replace=TRUE)
  samp2 <- sample(1:n, k, replace=TRUE)

  a1[sort(unique(samp1)), 1] <- as.numeric(table(samp1))
  a1[sort(unique(samp2)), 2] <- as.numeric(table(samp2))

  sum(rowSums(a1)==1)/n
}

ss<-(1:60)*5   #The grid of values of k for which we'll compute the probability.
a4<-matrix(NA,length(ss),2)
for(i in 1:length(ss)){
  a2<-ss[i]
  a3<-c(lapply(1:1000,fx02,n=100,k=a2),recursive=TRUE);
  a4[i,]<-c(a2,mean(a3))
}
plot(a4,xlab="k",ylab="frequency of distinct draw", pch=16, las=1)
abline(h=0.3697296, v=50)

max(a4[,2])
[1] 0.36971



Original answer
For the experiment 2 (with replacement), I think the probability that a certain number is drawn exactly once is:
$$
P_{\text{once}}=2k(n-1)^{(2k-1)}(1/n)^{2k}
$$
or
$$
P_{\text{once}}=2k(n-1)^{(2k-1)}n^{-2k}
$$
This can be checked by a simple example where $n=3$ and $k=2$. The probability to draw a certain number exactly once is in this case $2(4/9)^{2}\approx0.395$.
The maximum occurs of the formula above occurs for:
$$
k_{\text{max}}=\lfloor-\frac{1}{[2(\log(n + 1) + \log(1/n))]}\rceil
$$
or
$$
k_{\text{max}}=\lfloor-\frac{1}{[2(\log(n + 1) - \log(n))]}\rceil
$$
Where $k_{\text{max}}$ is rounded to the nearest integer. This is roughly $n/2$ for larger $n$, as already mentioned in the comments by @user603. For $n=100$, $k_{\text{max}}\approx 49.75$ so 50. The maximum probability for $n=100$ and $k_{\text{max}}=50$ would then be around $0.3697$ (as already worked out in the comments by @user603).
I set up a simulation to check this result in R:
prob.once <- vector()

draw.once <- function(n, k, sim=10000, repl=TRUE){

  for ( i in 1:sim ) {

    samp1 <- sample(1:n, size=k, replace=repl)
    samp2 <- sample(1:n, size=k, replace=repl)

    if ((is.element(1, samp1) & !is.element(1, samp2) & !is.element(1, samp1[duplicated(samp1)])) |
          (!is.element(1, samp1) & is.element(1, samp2) & !is.element(1, samp2[duplicated(samp2)])) ){
      prob.once[i] <- 1

    } else {
      prob.once[i] <- 0
    }    
  }      
  mean(prob.once)   
}

krepl <- 1:300
probs.repl <- sapply(krepl, FUN=draw.once, n=100, sim=20000, repl=TRUE)

plot(probs.repl~krepl, pch=16, type="p", lwd=2, las=1, ylab="Probability", xlab="k", col="steelblue")

abline(h=0.3697296)
abline(v=50)


The simulated result seems to confirm the above considerations.
