Multiple similarly named entities can all be removed by one of the removal commands. In AbstractRemoveCommand.java the patterns are dealt with via the following

for (final String key : existingProps.stringPropertyNames()) {
			if (key.startsWith(pattern)) {
				keysToRemove.add(key);
			}
		} 

The fact that it only checks the start of the entity names means that stores/indexes that start with the same letters can be removed by one call (i.e index1 and index2 would both be removed by calling geowave config rmindex index)