Hello & welcome,
, while doing clinical examination, can find these so called holes which are nothing but cavities. Or there may be pits which are more prone to decay & generally they may be treated with filling as a preventive measure.
Many times patient has no pain & dentist discovers carious spots or cavities which exactly has happened with you.
Remember one thing, when caries starts, it starts with zero pain but it progresses 24*7 & when caries crosses dentino enamel junction slight sensitivity to cold
If it is not treated at this stage with filling, it moves further decaying dentinal part of the tooth & finally reaches pulp or that vital part of the tooth which starts paining due to it.
If tooth is decayed but no pain, treatment is simple & straight forward, that is filling. If tooth is decayed & there is pain, treatment is more extensive ( in terms of cost & time taken ), that is Root canal treatment
So, it is very nice that your carious teeth are being diagnosed at early stage by your dentist. you can definitely go with filling or can have a second opinion
regarding this to confirm before filling.
And yes, i would advise, if a tooth is being diagnosed as decayed with no pain, then patient should never wait for pain to come..!