Does it matter if my book layout has runts?

There are no absolute rules for things like this. Yet somehow, over time, various suggestions and guidelines assume the status of absolute rules. The best advice I have seen is along the lines of "These are our recommendations for making pages. Break any of them if it makes pages look better." Then you ask, "What makes a page look bad?"

Setting runt control as a paragraph property (with a Grep style, as Eugene does) can cause a short paragraph to become very loose. Then you end up with a page (or spread) with unequal spacing. Which looks bad. (Sorry, Eugene.) It also conflicts with the good practice that all paragraphs on a spread should be spaced more or less evenly.

In fact, creating runts here and there can make spreads look better. On a spread where each paragraph's last line runs close to the right-hand margin can look like a solid black mass. Some runts create some breathing space.

It's the same with preventing the last word in a paragraph not to break. In languages like German and Dutch, which have many long words, that 'rule' is nonsense because, again, it causes very loose paragraphs. In English you can get away with it because it has far fewer long words. But even then you need longer paragraphs so that InDesign's paragraph composer has something too play with.

For such and similar reasons different traditions have developed in different countries, based on the characteristics of the written language. In Dutch typography, spacing is more important than avoiding word breaks, so Dutch setters have the spacing slider in the Hyphenation setings all the way to the left, at better spacing. (The same goes for German and, as far as I have seen so far, in Spanish too.) By the look of many books produced in English, that slider is all the way at 'fewer hyphens'.

A typesetter's concern should be how a spread looks, not necessarily whether all 'rules' have been followed. It's something you learn by experience, setting a lot of type, interacting with designers and production editors, and reading good books.

Two books that I can recommend are:

Finer points in the spacing & arrangement of type (Geoffrey Dowding)
The elements of typographic style (Robert Bringhurst)

In your example, the last word is hyphenated. This is Hyphenation Setting that you can turn off by deselecting Hyphenate Last Word.

But there are many cases when balancing justification, word spaces, and hyphenation rules that there may not be a clear cut best visual choice.

Not a deal breaker - but I don't like short words with Runts

For this reason I use this GREP find and replace

(?=\w{1,8}..?$)

Replace with 

~S

You could equally do it in the Paragraph style - and have a No Break characeter style and use this for the space

the 1,8 is for the length of the word

So words with 8 characters or less, longer words are ok for me. 

I wouldn't want them on every paragraph but but in a long publication a few of them are perfectly acceptable IMO.