and R.id=RC.id_rule
and RC.id_category=C.id

or r.categories.id in (select ...

or ONE OF r.categories IS CONTAINED IN (select ...

Only the important part:
select distinct r, s.weight, index(r)
from ProductDiscountRuleSet s inner join s.rules r
where ( (s.from = null and s.until = null)   
      or :now between s.from and s.until )
   and ( :customer in elements(r.customers)   
      or :priceFamily in elements(r.priceFamilies) )
   and ( :product in elements(r.products)   
      or (select p.brand from ProductI18N p join p.productReferences pr join pr.productReference prr where prr = :product) in elements(r.brands)   
      or r.categories.id in (select c.id from Category c join c.products cp join cp.productReferences cpr join cpr.productReference cprr where cprr = :product) )
order by s.weight, index(r)

select distinct R.id as col_0_0_, RS.weight as col_1_0_, R.ord as col_2_0_, R.id as id41_, R.version as version41_, R.stackable as stackable41_, R.last as last41_, R.discount as discount41_, R.fixed_amount_discount as fixed7_41_, R.fixed_price as fixed8_41_, R.base_price as base9_41_, R."unique" as unique10_41_, R.promotion as promotion41_, R.min_amount as min12_41_, R.free_shipping as free13_41_, R.paymentDelay as payment14_41_, R.discount_ref as discount15_41_, R.delay_ref as delay16_41_, R.type as type41_

from rule_sets RS inner join rules R
   on RS.id=R.id_rule_set, rules_categories RC, categories C
where
RS.type='P'
and R.id=RC.id_rule
and RC.id_category=C.id
and ((RS."from" is null)
   and (RS.until is null)
   or ? between RS."from" and RS.until)
and (? in (select RuleCust.id_customer
      from rules_customers RuleCust
      where R.id=RuleCust.id_rule)
   or ? in (select RulePriceFam.id_price_family
      from rules_price_families RulePriceFam
      where R.id=RulePriceFam.id_rule))
and (? in (select RuleProd.id_product
         from rules_product_references RuleProd
         where R.id=RuleProd.id_rule)
   or (select P.id_brand
         from products P inner join product_options O
               on P.id=O.id_product inner join product_references R
               on O.id_product_reference=R.id
         where R.id=?)
      in (select RuleBrand.id_brand
         from rules_brands RuleBrand
         where R.id=RuleBrand.id_rule)
   or C.id in (select C.id
         from categories C inner join products_catalogs PC
               on C.id=PC.id_category inner join products P
               on PC.id_product=P.id inner join product_options PO
               on P.id=PO.id_product inner join product_references PR
               on PO.id_product_reference=PR.id
         where PR.id=?))
order by RS.weight, R.ord

select distinct r, s.weight, index(r)
   from ProductDiscountRuleSet s inner join s.rules r left outer join r.categories SC
   where ( (s.from = null and s.until = null)
         or :now between s.from and s.until )
      and ( :customer in elements(r.customers)
         or :priceFamily in elements(r.priceFamilies) )
      and ( :product in elements(r.products)
         or (select p.brand from ProductI18N p join p.productReferences pr join
               pr.productReference prr where prr = :product) in elements(r.brands)
            or SC.id in (select c.id from Category c join c.products cp join cp.productReferences cpr
               join cpr.productReference cprr where cprr = :product) )
order by s.weight, index(r)