You can check if the contents are empty as well with an extra predicate. Optionally, you might want to ignore whitespace with normalize-space
:
<xsl:template match="n1:weitereAnmerkungen">
<xsl:if test="n1:table/n1:tbody/n1:tr/n1:td
and n1:table/n1:tbody/n1:tr/n1:td[normalize-space(.) != '']">
<xsl:apply-templates />
</xsl:if>
</xsl:template>