The first loop over k below is superfluous...it just loads each file into the same array but does nothing with it; then you start all over again immediately. Just delete that loop entirely.
for k = 1:length(matFiles)
matFilename = fullfile(myFolder, matFiles(k).name)
matData = load(matFilename);
end
for k = 1:length(matFiles)
matFilename = fullfile(myFolder, matFiles(k).name)
matData = load(matFilename);
...
Then, you need two things -- an accumulator for the means across the number of files by variable and to compute the mean for the entire array if, as it sounds, that is the wanted statistic--that needs the (:) Matlab idiom to return the full array regardless of dimensions/size as a single (column) vector:
vars={'ersp','itc'}; % variables wanted from .mat file
nF=length(matFiles); % how many files found?
mns=nan(nF,length(vars)); % allocate space; NaN so if missing won't plot 0
for k=1:nF
matFilename = fullfile(myFolder, matFiles(k).name); % fully-qualified file name
s=load(matFilename vars{:}); % load the desired variables in struct s
mns(k,:)=structfun(@(x) mean(x(:),'omitnan')).'; % compute means by file
end
Leaves you with the array of means for the variables in vars requested to plot as desired.
