SLDS enables developers to create a uniform look and feel across all Salesforce-related applications while adhering to CSS best practices and conventions.
Think about the folks using visualforce today who make their pages look like lightning via SLDS.
Lightning Base Components are not 'replacing' SLDS, instead they 'inherit' their styling from SLDS. Plus, SLDS is not limited to styling Lightning Base Components, as there are classes/guidelines that simply provide padding, margin, text, floats to name a few. SLDS is here to stay and is very actively managed even today. While it is true that not all Lightning Base Components have an SLDS equivalent today (well, not all will have them), we can certainly expect more equivalents to be added, as necessary, in upcoming releases.
And there is a lightning base component variant for a checkbox:
<lightning:input type="checkbox" label="Required option" name="input2" checked="true" required="true"/>
And, there is a fancier version of checkbox as well:
<lightning:input type="checkbox-button" label="Input Two" name="input2" checked="true" required="true"/>