Atkins says not to count them. Also, am reading Jacob Wilson and Ryan Lowery's The Ketogenic Bible: The Authoritative Guide to Ketosis (2017) - on net carbs:

Many people attempt to avoid carbohydrates altogether on a ketogenic diet. However, that also means avoiding fiber, which has important health benefits, especially for the gut. Dietary fibers are carbohydrates that are not broken down in the small intestine and instead make it to the large intestine, where they are broken down by bacteria. The great thing about fiber is that it has been shown to lower body fat, assist in managing diabetes, improve insulin sensitivity, decrease the risk of heart disease, elevate satiety, and foster beneficial bacteria in our guts (Slaving, 2013). Moreover, the fermentation of fiber in the gut produces short-chain fatty acids (SCFA), such as acetate, butyrate, and propionate, which are also ketogenic.

Research demonstrates that most individuals switching from a normal carbohydrate-based diet to a ketogenic diet drastically lower their fiber intake. In fact, one study found that decreasing carbohydrates from 400 to 23 grams daily also decreased fiber intake from 28 to 6 grams (Duncan et al., 2007). As a result, subjects decreased both their healthy bacteria as well as the production of healthy short-chain fatty acids. We believe it is paramount to maintain fiber intake on a ketogenic diet (by consuming green leafy vegetables and fibrous foods) and focus on reducing net carbohydrates; total carbohydrates minus fiber.

Several lines of evidence support focusing on net carbs instead of total carbs, but we will focus on just two of them. The first is that fiber, even though it is counted as a carbohydrate, should be resistant to digestion, so it does not increase blood glucose or insulin levels - and often lowers them (Slavin et al., 2013). Second, research shows that foods high in fiber could allow carbohydrates in the diet to be increased from 4-10 percent without hindering seizure control in epileptic patients (Pfeifer et al., 2005). Thus we suggest counting net carbs and including high-fiber foods in your diet. Green and cruciferous vegetables are great ways to add fiber and volume.

Resistant Starch and Butyrate

Resistant starches do exactly what their name implies: resist digestion. These types of starches have been shown to improve insulin sensitivity and reduce appetite. However, too much resistant starch can lead to bloating or GI discomfort due to the fact that it doesn't get digested. Once it's fermented by the bacteria in the gut, a short-chain fatty acid known as butyrate is produced. Butyrate is actually the preferred fuel of the cells that lline the colon, and there is a host of data showing its beneficial effects on human health and function. Finding ways to increase butyrate levels while lowering carbohydrates on a ketogenic diet can significantly improve gut bacteria and long-term success with the diet.