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Your approach is mostly OK, but I can see some points that could be improved:

• Having to assign sums to a variable so that you can map over its keys is ugly. Yes, there's no better way to that with builtin JS methods, but this thing should be factored out into a helper function
• Instead of using forEach, you can nest reduce calls. Or just use a simple for in loop over each object's properties - it doesn't matter, you have to execute side effects anyway.
• Instead of starting with an empty object, you could start with an object where all the known properties are initialised to nothing. That would avoid the hasOwnProperty check (which, as you have written it, is fragile anyway).
• You have a bug for the case that data.length is 0 - Object.keys will fail.
• Don't put the console.log inside summary, put it around the call and return your averages. Also I'm not sure where this.data comes from, better take it as a parameter.

function mapObject(o, fn) {
 return Object.keys(o).map(k => fn(o[k], k));
}
function summary(data) {
 if (!data.length) return {};
 var keys = Object.keys(data[0]);
 return mapObject(data.reduce((previous, element) => {
 return keys.reduce((previous, k) => {
 if (element[k] != null) {
 previous[k].value += element[k];
 previous[k].count += 1;
 }
 return previous;
 }, previous);
 }, keys.reduce(function(sums, k) {
 sums[k] = {value: 0, count: 0};
 return sums;
 }, {})), (x, name) => ({
 name,
 average: x.value / x.count
 }));
}

or

function summary(data) {
 return mapObject(data.reduce((previous, element) => {
 for (k in element) {
 if (element[k] == null) continue;
 if (k in previous) {
 previous[k].value += element[k];
 previous[k].count += 1;
 } else {
 previous[k] = { value: element[k], count: 1 };
 }
 }
 return previous;
 }, {}), (x, name) => ({
 name,
 average: x.value / x.count
 }));
}